refactor!: delete the input.link runtime mirror

The linkStore is now the single source for slot connectivity in both
directions. The NodeInputSlot.link field and all runtime write sites are
gone; a read-only prototype getter derives the id from the store and
fires warnDeprecated as extension migration telemetry (no setter, so
writes throw). Wire format unchanged: serialization derives
inputs[].link from the store.

The mirror-carried association machinery is reworked rather than
papered over: fixLinkInputSlots consumes the serialized graph data
(where node.configure reorders inputs in place), dynamicWidgets' group
rebuilds carry slot-to-link association in a WeakMap refreshed from the
store, reorderSubgraphInputs captures outer links by pre-reorder index,
and link deduplication selects survivors from the store registration -
repairInputLinks is deleted because the derived view cannot be
inconsistent.

Extension migration: read via node.isInputConnected(slot) /
node.getInputLink(slot); mutate via node.connect() /
node.disconnectInput().

docs/architecture/link-topology-store.md

@@ -105,11 +105,9 @@ subgraph-definition GC unregister whole graphs
 
 This design covers link topology (endpoints, type, chain terminus).
 Link visual state (`color`, path caches) and the layout store's link
-_geometry_ records are out of scope. The `output.links` mirror has since
-been deleted — the store is the single source for output-side
-connectivity (see
-[output slot connectivity](output-slot-connectivity.md) Decision 6). The
-`input.link` slot mirror remains the litegraph-native representation
-un-migrated consumers read; extracting it is the `SlotConnection`
-component work in the [ECS migration plan](ecs-migration-plan.md), not
-part of this store.
+_geometry_ records are out of scope. The `output.links` and `input.link`
+slot mirrors have since been deleted — the store is the single source
+for slot connectivity in both directions (see
+[output slot connectivity](output-slot-connectivity.md) Decision 6);
+the remaining fields are deprecated warning getters kept as extension
+migration telemetry.

docs/architecture/output-slot-connectivity.md

@@ -123,10 +123,20 @@ a mirror read plus a `slotFloatingLinks` scan), widget value propagation
 (`widgetValuePropagation`), and matchType link revalidation
 (`dynamicWidgets.changeOutputType`).
 
-## Decision 6: Delete the mirror (implemented)
+## Decision 6: Delete the mirrors (implemented; extended to `input.link`)
 
 The runtime `output.links[]` field and all nine of its write sites are
-deleted. The store is the single source; litegraph internals read through
+deleted. The same recipe has since been applied to `input.link`: the
+field is a deprecated warning getter, litegraph and app code read through
+the slotLinks input helpers (`inputHasLink`, `inputLinkId`, `inputLink`)
+or `node.isInputConnected` / `node.getInputLink`, serialization derives
+`inputs[].link` from the store, and the mirror-carried association
+shuffles were reworked — `fixLinkInputSlots` consumes the serialized
+graph data, dynamicWidgets' group rebuilds carry slot→link association
+in a module-scoped WeakMap refreshed from the store, and link
+deduplication selects survivors from the store registration (the
+`repairInputLinks` mirror repair is gone; the derived view cannot be
+wrong). The store is the single source; litegraph internals read through
 the pure helpers in `node/slotLinks.ts` (`outputHasLinks`,
 `outputLinkIds`, `outputLinks`), and `NodeOutputSlot.isConnected`,
 `serialize`, and `configure` derive from the store. Details:
@@ -193,7 +203,6 @@ sites, and field deletion.
 
 Out of scope, each a piece of the deferred `SlotConnection` phase:
 
-- Deleting the `input.link` mirror field (same recipe as Decision 6).
 - Slot entity extraction: `SlotIdentity`, `SlotVisual`, and retiring the
   `NodeInputSlot` / `NodeOutputSlot` class instances and their
   `shallowReactive` graft.

src/core/graph/widgets/dynamicWidgets.test.ts

@@ -1,6 +1,6 @@
 import { setActivePinia } from 'pinia'
 import { createTestingPinia } from '@pinia/testing'
-import { describe, expect, test, vi } from 'vitest'
+import { beforeEach, describe, expect, test, vi } from 'vitest'
 import { LGraph, LGraphNode } from '@/lib/litegraph/src/litegraph'
 import { transformInputSpecV1ToV2 } from '@/schemas/nodeDef/migration'
 import type { InputSpec } from '@/schemas/nodeDefSchema'
@@ -8,6 +8,7 @@ import { useLitegraphService } from '@/services/litegraphService'
 import type { HasInitialMinSize } from '@/services/litegraphService'
 
 setActivePinia(createTestingPinia({ stubActions: false }))
+beforeEach(() => setActivePinia(createTestingPinia({ stubActions: false })))
 type DynamicInputs = ('INT' | 'STRING' | 'IMAGE' | DynamicInputs)[][]
 type TestAutogrowNode = LGraphNode & {
   comfyDynamic: { autogrow: Record<string, unknown> }

src/core/graph/widgets/dynamicWidgets.ts

@@ -22,6 +22,7 @@ import {
 import { useLitegraphService } from '@/services/litegraphService'
 import { app } from '@/scripts/app'
 import type { ComfyApp } from '@/scripts/app'
+import { inputLink } from '@/lib/litegraph/src/node/slotLinks'
 import { useLinkStore } from '@/stores/linkStore'
 import { useWidgetValueStore } from '@/stores/widgetValueStore'
 import { widgetId } from '@/types/widgetId'
@@ -109,6 +110,7 @@ function dynamicComboWidget(
     if (!node.widgets) throw new Error('Not Reachable')
     const newSpec = value ? options[value] : undefined
 
+    captureCarriedLinks(node)
     const removedInputs = remove(node.inputs, isInGroup)
     for (const widget of remove(node.widgets, isInGroup)) {
       widget.onRemove?.()
@@ -178,13 +180,12 @@ function dynamicComboWidget(
 
     for (const input of removedInputs) {
       const inputIndex = node.inputs.findIndex((inp) => inp.name === input.name)
+      const link = carriedLink(node, input)
       if (inputIndex === -1) {
+        if (link) node.graph?.removeLink(link.id)
         node.inputs.push(input)
         node.removeInput(node.inputs.length - 1)
       } else {
-        node.inputs[inputIndex].link = input.link
-        if (!input.link) continue
-        const link = node.graph?.links?.[input.link]
         if (!link) continue
         link.target_slot = inputIndex
         node.onConnectionsChange?.(
@@ -247,16 +248,39 @@ export function applyDynamicInputs(
   return true
 }
 
+/**
+ * Slot-object → link association carried across the group rebuild shuffles.
+ * The deleted `input.link` mirror used to travel with the slot object; this
+ * registry replaces it for the duration of a rebuild, refreshed from the
+ * link store whenever the inputs array is at rest.
+ */
+const carriedLinks = new WeakMap<INodeInputSlot, LLink>()
+
+function captureCarriedLinks(node: LGraphNode) {
+  const { graph } = node
+  if (!graph) return
+  for (const [index, input] of node.inputs.entries()) {
+    const link = inputLink(graph, node.id, index)
+    if (link) carriedLinks.set(input, link)
+  }
+}
+
+function carriedLink(node: LGraphNode, input: INodeInputSlot) {
+  const link = carriedLinks.get(input)
+  return link && node.graph?.getLink(link.id) ? link : undefined
+}
+
 function spliceInputs(
   node: LGraphNode,
   startIndex: number,
   deleteCount = -1,
   ...toAdd: INodeInputSlot[]
 ): INodeInputSlot[] {
+  captureCarriedLinks(node)
   if (deleteCount < 0) return node.inputs.splice(startIndex)
   const ret = node.inputs.splice(startIndex, deleteCount, ...toAdd)
   node.inputs.slice(startIndex).forEach((input, index) => {
-    const link = input.link && node.graph?.links?.get(input.link)
+    const link = carriedLink(node, input)
     if (link) link.target_slot = startIndex + index
   })
   return ret
@@ -384,11 +408,12 @@ function applyMatchType(node: LGraphNode, inputSpec: InputSpecV2) {
     const input = node.inputs[index]
     if (!input) return
     node.inputs[index] = shallowReactive(input)
+    const existingLink = node.getInputLink(index)
     node.onConnectionsChange?.(
       LiteGraph.INPUT,
       index,
-      !!input.link,
-      input.link ? node.graph?.links?.[input.link] : undefined,
+      !!existingLink,
+      existingLink ?? undefined,
       input
     )
   })
@@ -440,7 +465,10 @@ function addAutogrowGroup(
       (inp) => inp.name === newInput.name
     )) {
       //NOTE: link.target_slot is updated on spliceInputs call
-      newInput.link ??= existingInput.link
+      const carried = carriedLinks.get(existingInput)
+      if (carried && !carriedLinks.has(newInput)) {
+        carriedLinks.set(newInput, carried)
+      }
     }
   }
 
@@ -516,6 +544,13 @@ function autogrowInputDisconnected(index: number, node: AutogrowNode) {
     return
   }
   app.canvas?.setDirty(true, true)
+  // Snapshot each group slot's link before shuffling: donors are always read
+  // pre-shuffle, matching the sequential copy the mirror used to perform.
+  const linkByOrdinal = groupInputs.map((inp) =>
+    node.graph
+      ? inputLink(node.graph, node.id, node.inputs.indexOf(inp))
+      : undefined
+  )
   //groupBy would be nice here, but may not be supported
   for (let column = 0; column < stride; column++) {
     for (
@@ -524,9 +559,7 @@ function autogrowInputDisconnected(index: number, node: AutogrowNode) {
       bubbleOrdinal += stride
     ) {
       const curInput = groupInputs[bubbleOrdinal]
-      curInput.link = groupInputs[bubbleOrdinal + stride].link
-      if (!curInput.link) continue
-      const link = node.graph?.links[curInput.link]
+      const link = linkByOrdinal[bubbleOrdinal + stride]
       if (!link) continue
       const curIndex = node.inputs.findIndex((inp) => inp === curInput)
       if (curIndex === -1) throw new Error('missing input')
@@ -541,7 +574,6 @@ function autogrowInputDisconnected(index: number, node: AutogrowNode) {
     }
     const lastInput = groupInputs.at(column - stride)
     if (!lastInput) continue
-    lastInput.link = null
     node.onConnectionsChange?.(
       LiteGraph.INPUT,
       node.inputs.length + column - stride,
@@ -553,7 +585,12 @@ function autogrowInputDisconnected(index: number, node: AutogrowNode) {
   const removalChecks = groupInputs.slice(min * stride)
   let i
   for (i = removalChecks.length - stride; i >= 0; i -= stride) {
-    if (removalChecks.slice(i, i + stride).some((inp) => inp.link)) break
+    if (
+      removalChecks
+        .slice(i, i + stride)
+        .some((inp) => node.isInputConnected(node.inputs.indexOf(inp)))
+    )
+      break
   }
   const toRemove = removalChecks.slice(i + stride * 2)
   remove(node.inputs, (inp) => toRemove.includes(inp))

src/lib/litegraph/src/LGraph.test.ts

@@ -1004,19 +1004,21 @@ describe('_removeDuplicateLinks', () => {
     expect(graph._links.size).toBe(1)
     expect(graph._links.has(validLinkId)).toBe(true)
     expect(graph._links.has(dupLink.id)).toBe(false)
-    expect(target.inputs[1].link).toBe(validLinkId)
+    const store = useLinkStore()
+    expect(store.getInputSlotLink(graph.rootGraph.id, target.id, 0)?.id).toBe(
+      validLinkId
+    )
   })
 
-  it('repairs input.link when it points to a removed duplicate', () => {
+  it('derives input.link from the surviving registration after dedup', () => {
     const { graph, source, target } = createConnectedGraph()
 
     const dupLink = injectDuplicateLink(graph, source, target)
-    // Point input.link to the duplicate (simulating corrupted state)
-    target.inputs[0].link = dupLink.id
 
     graph._removeDuplicateLinks()
 
     expect(graph._links.size).toBe(1)
+    expect(graph._links.has(dupLink.id)).toBe(false)
     const survivingId = graph._links.keys().next().value!
     expect(target.inputs[0].link).toBe(survivingId)
     expect(graph._links.has(target.inputs[0].link!)).toBe(true)

src/lib/litegraph/src/LGraph.ts

@@ -25,7 +25,6 @@ import { forEachNode } from '@/utils/graphTraversalUtil'
 import {
   groupLinksByTuple,
   purgeOrphanedLinks,
-  repairInputLinks,
   selectSurvivorLink
 } from './linkDeduplication'
 
@@ -1707,7 +1706,6 @@ export class LGraph
       const keepId = selectSurvivorLink(ids, node)
 
       purgeOrphanedLinks(ids, keepId, this)
-      repairInputLinks(ids, keepId, node)
     }
   }
 

src/lib/litegraph/src/LGraphCanvas.drawConnections.test.ts

@@ -80,7 +80,6 @@ function createTestLink(
     inputSlot
   )
   graph._addLink(link)
-  targetNode.inputs[inputSlot].link = linkId
   return link
 }
 

src/lib/litegraph/src/LGraphNode.ts

@@ -2983,9 +2983,7 @@ export class LGraphNode
     // add to graph links list
     graph._addLink(link)
 
-    // connect in input
     const targetInput = inputNode.inputs[inputIndex]
-    targetInput.link = link.id
     if (targetInput.widget) {
       graph.trigger('node:slot-links:changed', {
         nodeId: inputNode.id,
@@ -3128,8 +3126,6 @@ export class LGraphNode
 
         // is the link we are searching for...
         const input = target.inputs[link_info.target_slot]
-        // remove there
-        input.link = null
         if (input.widget) {
           graph.trigger('node:slot-links:changed', {
             nodeId: target.id,
@@ -3182,8 +3178,6 @@ export class LGraphNode
 
         if (target) {
           const input = target.inputs[link_info.target_slot]
-          // remove other side link
-          input.link = null
           if (input.widget) {
             graph.trigger('node:slot-links:changed', {
               nodeId: target.id,
@@ -3258,7 +3252,6 @@ export class LGraphNode
 
     const link_id = inputLinkId(graph, this.id, slot) ?? null
     if (link_id != null) {
-      this.inputs[slot].link = null
       if (input.widget) {
         graph.trigger('node:slot-links:changed', {
           nodeId: this.id,

src/lib/litegraph/src/interfaces.ts

@@ -360,7 +360,13 @@ export interface IWidgetLocator {
 }
 
 export interface INodeInputSlot extends INodeSlot {
-  link: LinkId | null
+  /**
+   * @deprecated Id of the link targeting this slot, derived from the link
+   * store by a warning getter. Read via `node.isInputConnected(slot)` /
+   * `node.getInputLink(slot)`; mutate via `node.connect()` /
+   * `node.disconnectInput()`.
+   */
+  readonly link?: LinkId | null
   widget?: IWidgetLocator
   widgetId?: WidgetId
   alwaysVisible?: boolean

src/lib/litegraph/src/linkDeduplication.ts

@@ -1,4 +1,5 @@
 import { registerLinkTopology } from './LLink'
+import { inputLinkId } from './node/slotLinks'
 
 import type { LGraph } from './LGraph'
 import type { LGraphNode } from './LGraphNode'
@@ -31,12 +32,11 @@ export function selectSurvivorLink(
   ids: LinkId[],
   node: LGraphNode | null
 ): LinkId {
-  if (!node) return ids[0]
+  if (!node?.graph) return ids[0]
 
-  for (const input of node.inputs ?? []) {
-    if (!input) continue
-    const match = ids.find((id) => input.link === id)
-    if (match != null) return match
+  for (const [index] of (node.inputs ?? []).entries()) {
+    const registered = inputLinkId(node.graph, node.id, index)
+    if (registered != null && ids.includes(registered)) return registered
   }
   return ids[0]
 }
@@ -65,21 +65,3 @@ export function purgeOrphanedLinks(
   const survivor = graph._links.get(keepId)
   if (survivor) registerLinkTopology(graph, survivor)
 }
-
-/** Ensures input.link on the target node points to the surviving link. */
-export function repairInputLinks(
-  ids: LinkId[],
-  keepId: LinkId,
-  node: LGraphNode | null
-): void {
-  if (!node) return
-
-  const duplicateIds = new Set(ids)
-
-  for (const input of node.inputs ?? []) {
-    if (input?.link == null || input.link === keepId) continue
-    if (duplicateIds.has(input.link)) {
-      input.link = keepId
-    }
-  }
-}

src/lib/litegraph/src/node/NodeInputSlot.ts

@@ -10,6 +10,7 @@ import type {
 import { LiteGraph } from '@/lib/litegraph/src/litegraph'
 import { NodeSlot } from '@/lib/litegraph/src/node/NodeSlot'
 import { inputHasLink, inputLinkId } from '@/lib/litegraph/src/node/slotLinks'
+import { warnDeprecated } from '@/lib/litegraph/src/utils/feedback'
 import type { IDrawOptions } from '@/lib/litegraph/src/node/NodeSlot'
 import type { SubgraphInput } from '@/lib/litegraph/src/subgraph/SubgraphInput'
 import type { SubgraphOutput } from '@/lib/litegraph/src/subgraph/SubgraphOutput'
@@ -17,7 +18,8 @@ import { isSubgraphInput } from '@/lib/litegraph/src/subgraph/subgraphUtils'
 import type { IBaseWidget } from '@/lib/litegraph/src/types/widgets'
 
 export class NodeInputSlot extends NodeSlot implements INodeInputSlot {
-  link: LinkId | null
+  /** @deprecated Derived from the link store via a warning prototype getter; never written. */
+  declare readonly link?: LinkId | null
   alwaysVisible?: boolean
 
   get isWidgetInputSlot(): boolean {
@@ -43,8 +45,11 @@ export class NodeInputSlot extends NodeSlot implements INodeInputSlot {
     slot: OptionalProps<INodeInputSlot, 'boundingRect'>,
     node: LGraphNode
   ) {
-    super(slot, node)
-    this.link = slot.link
+    // Serialized inputs carry a legacy link mirror; strip it so the base
+    // ctor's Object.assign cannot collide with the deprecated prototype
+    // getter (assigning a getter-only property throws in strict mode).
+    const { link: _legacyLink, ...rest } = slot
+    super(rest, node)
   }
 
   override get isConnected(): boolean {
@@ -95,3 +100,23 @@ export class NodeInputSlot extends NodeSlot implements INodeInputSlot {
     }
   }
 }
+
+/**
+ * Deprecation telemetry for extensions that still read `input.link`.
+ * Returns the store-derived link id; there is deliberately no setter, so
+ * writes throw in strict mode. First-party code uses the slotLinks helpers.
+ */
+Object.defineProperty(NodeInputSlot.prototype, 'link', {
+  get(this: NodeInputSlot): LinkId | null {
+    warnDeprecated(
+      'input.link is deprecated. Read connectivity via node.isInputConnected(slot) / node.getInputLink(slot); mutate via node.connect() / node.disconnectInput().'
+    )
+    const { graph } = this._node
+    if (!graph) return null
+    return (
+      inputLinkId(graph, this._node.id, this._node.inputs.indexOf(this)) ?? null
+    )
+  },
+  configurable: true,
+  enumerable: false
+})

src/lib/litegraph/src/subgraph/SubgraphInput.ts

@@ -120,7 +120,6 @@ export class SubgraphInput extends SubgraphSlot {
 
     // Set link ID in each slot
     this.linkIds.push(link.id)
-    slot.link = link.id
 
     anchorRerouteChain(subgraph, link)
     subgraph.incrementVersion()

src/lib/litegraph/src/subgraph/SubgraphInputNode.ts

@@ -189,7 +189,6 @@ export class SubgraphInputNode
       subgraph.removeFloatingLink(floatingLink)
     }
 
-    input.link = null
     subgraph.setDirtyCanvas(false, true)
 
     if (!link) return

src/lib/litegraph/src/subgraph/subgraphUtils.ts

@@ -4,7 +4,11 @@ import { LGraphGroup } from '@/lib/litegraph/src/LGraphGroup'
 import { LGraphNode } from '@/lib/litegraph/src/LGraphNode'
 import { LLink, slotFloatingLinks } from '@/lib/litegraph/src/LLink'
 import type { ResolvedConnection } from '@/lib/litegraph/src/LLink'
-import { inputLinkId, outputLinkIds } from '@/lib/litegraph/src/node/slotLinks'
+import {
+  inputLink,
+  inputLinkId,
+  outputLinkIds
+} from '@/lib/litegraph/src/node/slotLinks'
 import { Reroute } from '@/lib/litegraph/src/Reroute'
 import type { RerouteId } from '@/lib/litegraph/src/Reroute'
 import { toRerouteId } from '@/types/rerouteId'
@@ -530,6 +534,14 @@ export function reorderSubgraphInputs(
 
   const oldOrder = subgraph.inputs.map((i) => i.id)
 
+  // Capture outer links by pre-reorder index: the store is keyed by
+  // target_slot, which the physical reorder does not move.
+  const outerLinks = subgraphNode.inputs.map((_input, index) =>
+    subgraphNode.graph
+      ? inputLink(subgraphNode.graph, subgraphNode.id, index)
+      : undefined
+  )
+
   reorderInPlace(subgraph.inputs, orderedIndices)
   reorderInPlace(subgraphNode.inputs, orderedIndices)
   subgraphNode.invalidatePromotedViews()
@@ -541,11 +553,9 @@ export function reorderSubgraphInputs(
     link.origin_slot = slot
   }
 
-  function* outerLink(input: INodeInputSlot): Generator<LLink | undefined> {
-    if (input.link != null) yield subgraphNode.graph?.getLink(input.link)
-  }
-  for (const [slot, link] of indexedLinks(subgraphNode.inputs, outerLink)) {
-    link.target_slot = slot
+  for (const [newIndex, oldIndex] of orderedIndices.entries()) {
+    const link = outerLinks[oldIndex]
+    if (link) link.target_slot = newIndex
   }
 
   const newOrder = subgraph.inputs.map((i) => i.id)

src/platform/nodeReplacement/useNodeReplacement.test.ts

@@ -269,7 +269,6 @@ describe('useNodeReplacement', () => {
       // Link should be updated to point at new node's input
       expect(link.target_id).toBe(1)
       expect(link.target_slot).toBe(0)
-      expect(newNode.inputs[0].link).toBe(10)
     })
 
     it('should transfer output connections using output_mapping', () => {
@@ -655,7 +654,8 @@ describe('useNodeReplacement', () => {
 
       // Default mapping transfers connections and widget values by name
       expect(newNode.id).toBe(13)
-      expect(newNode.inputs[0].link).toBe(4)
+      expect(link.target_id).toBe(13)
+      expect(link.target_slot).toBe(0)
       expect(outLink.origin_id).toBe(13)
       expect(outLink.origin_slot).toBe(0)
       expect(newNode.widgets![0].value).toBe(0.75)

src/platform/nodeReplacement/useNodeReplacement.ts

@@ -51,8 +51,6 @@ function transferInputConnection(
 
   link.target_id = newNode.id
   link.target_slot = newSlotIdx
-  newNode.inputs[newSlotIdx].link = linkId
-  oldNode.inputs[oldSlotIdx].link = null
 }
 
 function transferOutputConnections(

src/scripts/app.ts

@@ -863,7 +863,8 @@ export class ComfyApp {
       }
 
       try {
-        fixLinkInputSlots(this)
+        const [configuredData] = args
+        if (configuredData) fixLinkInputSlots(this, configuredData)
 
         // Fire callbacks before the onConfigure, this is used by widget inputs to setup the config
         triggerCallbackOnAllNodes(this, 'onGraphConfigured')

src/utils/linkFixer.test.ts

@@ -326,7 +326,7 @@ describe('fixBadLinks', () => {
 describe('fixBadLinks ↔ linkStore integration', () => {
   beforeEach(() => setActivePinia(createTestingPinia({ stubActions: false })))
 
-  it('completes the input mirror for a registered link missing it', () => {
+  it('treats a store-registered link as consistent without repairs', () => {
     const graph = new LGraph()
     const a = new LGraphNode('A')
     const b = new LGraphNode('B')
@@ -335,20 +335,19 @@ describe('fixBadLinks ↔ linkStore integration', () => {
     graph.add(a)
     graph.add(b)
 
-    // Registered via the chokepoint, but the input mirror was never written.
-    const orphan = new LLink(toLinkId(9), '*', a.id, 0, b.id, 0)
-    graph._addLink(orphan)
+    // Registered via the chokepoint; slot views derive from the store.
+    const link = new LLink(toLinkId(9), '*', a.id, 0, b.id, 0)
+    graph._addLink(link)
 
     const store = useLinkStore()
     const graphId = graph.rootGraph.id
     expect(store.isInputSlotConnected(graphId, b.id, 0)).toBe(true)
-    expect(b.inputs[0].link).toBeNull()
+    expect(b.inputs[0].link).toBe(link.id)
 
     const result = fixBadLinks(graph, { fix: true, silent: true })
 
-    expect(result).toMatchObject({ fixed: true, patched: 1, deleted: 0 })
-    expect(graph._links.has(orphan.id)).toBe(true)
-    expect(b.inputs[0].link).toBe(orphan.id)
+    expect(result).toMatchObject({ hasBadLinks: false, deleted: 0 })
+    expect(graph._links.has(link.id)).toBe(true)
     expect(store.isInputSlotConnected(graphId, b.id, 0)).toBe(true)
   })
 })

src/utils/linkFixer.ts

@@ -25,6 +25,7 @@
  * SOFTWARE.
  */
 import type { INodeOutputSlot } from '@/lib/litegraph/src/interfaces'
+import { NodeInputSlot } from '@/lib/litegraph/src/node/NodeInputSlot'
 import { NodeOutputSlot } from '@/lib/litegraph/src/node/NodeOutputSlot'
 import { toLinkId } from '@/types/linkId'
 import { parseNodeId } from '@/types/nodeId'
@@ -148,8 +149,11 @@ export function fixBadLinks(
         return false
       }
       patchedNode['inputs']![slot] = linkIdToSet
-      if (fix) {
-        inputSlot!.link = linkIdToSet === null ? null : toLinkId(linkIdToSet)
+      // Live NodeInputSlot mirrors are store-derived and need no repair;
+      // only serialized plain slots carry a writable link field.
+      if (fix && !(inputSlot instanceof NodeInputSlot)) {
+        const writable = inputSlot as { link?: number | null }
+        writable.link = linkIdToSet
       }
     } else {
       patchedNode['outputs'] = patchedNode['outputs'] || {}

src/utils/litegraphUtil.ts

@@ -1,6 +1,7 @@
 import _ from 'es-toolkit/compat'
 
 import type { ColorOption, LGraph } from '@/lib/litegraph/src/litegraph'
+import { toLinkId } from '@/types/linkId'
 import type { ExecutedWsMessage } from '@/schemas/apiSchema'
 import {
   LGraphCanvas,
@@ -13,7 +14,8 @@ import {
 import type {
   ExportedSubgraph,
   ISerialisableNodeInput,
-  ISerialisedGraph
+  ISerialisedGraph,
+  SerialisableGraph
 } from '@/lib/litegraph/src/types/serialisation'
 import type {
   IBaseWidget,
@@ -234,25 +236,29 @@ export function migrateWidgetsValues<TWidgetValue>(
  *
  * @param graph - The graph to fix links for.
  */
-export function fixLinkInputSlots(graph: LGraph) {
-  // Note: We can't use forEachNode here because we need access to the graph's
-  // links map at each level. Links are stored in their respective graph/subgraph.
-  for (const node of graph.nodes) {
-    // Fix links for the current node
-    for (const [inputIndex, input] of node.inputs.entries()) {
-      const linkId = input.link
-      if (!linkId) continue
+export function fixLinkInputSlots(
+  graph: LGraph,
+  data: ISerialisedGraph | SerialisableGraph
+) {
+  // The slot association lives in the serialized node data: node.configure
+  // reorders each serialized inputs array to definition order in place, and
+  // each entry still carries the link id it was saved with. Links are stored
+  // in their respective graph/subgraph.
+  for (const serialisedNode of data.nodes ?? []) {
+    for (const [inputIndex, input] of (serialisedNode.inputs ?? []).entries()) {
+      if (input.link == null) continue
 
-      const link = graph.links.get(linkId)
+      const link = graph.links.get(toLinkId(input.link))
       if (!link) continue
 
       link.target_slot = inputIndex
     }
+  }
 
-    // Recursively fix links in subgraphs
-    if (node.isSubgraphNode?.() && node.subgraph) {
-      fixLinkInputSlots(node.subgraph)
-    }
+  // Recursively fix links in subgraph definitions
+  for (const subgraphData of data.definitions?.subgraphs ?? []) {
+    const subgraph = graph.rootGraph.subgraphs.get(subgraphData.id)
+    if (subgraph) fixLinkInputSlots(subgraph, subgraphData)
   }
 }