diff --git a/src/lib/litegraph/src/LGraphCanvas.ts b/src/lib/litegraph/src/LGraphCanvas.ts
index 37c0950a2..a56627064 100644
--- a/src/lib/litegraph/src/LGraphCanvas.ts
+++ b/src/lib/litegraph/src/LGraphCanvas.ts
@@ -5614,6 +5614,9 @@ export class LGraphCanvas implements CustomEventDispatcher<LGraphCanvasEventMap>
     this.renderedPaths.clear()
     if (this.links_render_mode === LinkRenderType.HIDDEN_LINK) return
 
+    // Skip link rendering while waiting for slot positions to sync after reconfigure
+    if (LiteGraph.vueNodesMode && layoutStore.pendingSlotSync) return
+
     const { graph, subgraph } = this
     if (!graph) throw new NullGraphError()
 
diff --git a/src/renderer/core/layout/store/layoutStore.ts b/src/renderer/core/layout/store/layoutStore.ts
index 786be0625..ed928bb00 100644
--- a/src/renderer/core/layout/store/layoutStore.ts
+++ b/src/renderer/core/layout/store/layoutStore.ts
@@ -141,6 +141,20 @@ class LayoutStoreImpl implements LayoutStore {
   // Vue resizing state to prevent drag from activating during resize
   public isResizingVueNodes = ref(false)
 
+  /**
+   * Flag indicating slot positions are pending sync after graph reconfiguration.
+   * When true, link rendering should be skipped to avoid drawing with stale positions.
+   */
+  private _pendingSlotSync = false
+
+  get pendingSlotSync(): boolean {
+    return this._pendingSlotSync
+  }
+
+  setPendingSlotSync(value: boolean): void {
+    this._pendingSlotSync = value
+  }
+
   constructor() {
     // Initialize Yjs data structures
     this.ynodes = this.ydoc.getMap('nodes')
diff --git a/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts b/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts
index c92fc8c92..9f355f9fd 100644
--- a/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts
+++ b/src/renderer/extensions/vueNodes/composables/useSlotElementTracking.ts
@@ -31,13 +31,19 @@ function scheduleSlotLayoutSync(nodeId: string) {
   raf.schedule()
 }
 
-function flushScheduledSlotLayoutSync() {
-  if (pendingNodes.size === 0) return
+export function flushScheduledSlotLayoutSync() {
+  if (pendingNodes.size === 0) {
+    // Even if no pending nodes, clear the flag (e.g., graph with no nodes)
+    layoutStore.setPendingSlotSync(false)
+    return
+  }
   const conv = useSharedCanvasPositionConversion()
   for (const nodeId of Array.from(pendingNodes)) {
     pendingNodes.delete(nodeId)
     syncNodeSlotLayoutsFromDOM(nodeId, conv)
   }
+  // Clear the pending sync flag - slots are now synced
+  layoutStore.setPendingSlotSync(false)
 }
 
 export function syncNodeSlotLayoutsFromDOM(
diff --git a/src/scripts/app.ts b/src/scripts/app.ts
index 796965b27..b5ac60349 100644
--- a/src/scripts/app.ts
+++ b/src/scripts/app.ts
@@ -5,6 +5,8 @@ import { reactive, unref } from 'vue'
 import { shallowRef } from 'vue'
 
 import { useCanvasPositionConversion } from '@/composables/element/useCanvasPositionConversion'
+import { layoutStore } from '@/renderer/core/layout/store/layoutStore'
+import { flushScheduledSlotLayoutSync } from '@/renderer/extensions/vueNodes/composables/useSlotElementTracking'
 import { registerProxyWidgets } from '@/core/graph/subgraph/proxyWidget'
 import { st, t } from '@/i18n'
 import type { IContextMenuValue } from '@/lib/litegraph/src/interfaces'
@@ -730,6 +732,11 @@ export class ComfyApp {
   private addAfterConfigureHandler(graph: LGraph) {
     const { onConfigure } = graph
     graph.onConfigure = function (...args) {
+      // Set pending sync flag to suppress link rendering until slots are synced
+      if (LiteGraph.vueNodesMode) {
+        layoutStore.setPendingSlotSync(true)
+      }
+
       fixLinkInputSlots(this)
 
       // Fire callbacks before the onConfigure, this is used by widget inputs to setup the config
@@ -740,6 +747,12 @@ export class ComfyApp {
       // Fire after onConfigure, used by primitives to generate widget using input nodes config
       triggerCallbackOnAllNodes(this, 'onAfterGraphConfigured')
 
+      // Flush pending slot layout syncs to fix link alignment after undo/redo
+      if (LiteGraph.vueNodesMode) {
+        flushScheduledSlotLayoutSync()
+        app.canvas?.setDirty(true, true)
+      }
+
       return r
     }
   }