diff --git a/browser_tests/fixtures/utils/builderTestUtils.ts b/browser_tests/fixtures/utils/builderTestUtils.ts
index 720b0685e7..b45978cd5f 100644
--- a/browser_tests/fixtures/utils/builderTestUtils.ts
+++ b/browser_tests/fixtures/utils/builderTestUtils.ts
@@ -122,3 +122,19 @@ export async function saveAndReopenInAppMode(
 
   await comfyPage.appMode.toggleAppMode()
 }
+
+export async function saveCloseAndReopenInBuilder(
+  comfyPage: ComfyPage,
+  appMode: AppModeHelper,
+  workflowName: string
+) {
+  await appMode.steps.goToPreview()
+  await builderSaveAs(appMode, workflowName)
+  await appMode.saveAs.closeButton.click()
+  await expect(appMode.saveAs.successDialog).toBeHidden()
+
+  await appMode.footer.exitBuilder()
+  await openWorkflowFromSidebar(comfyPage, workflowName)
+  await appMode.enterBuilder()
+  await appMode.steps.goToInputs()
+}
diff --git a/browser_tests/tests/appModeInputPersistence.spec.ts b/browser_tests/tests/appModeInputPersistence.spec.ts
new file mode 100644
index 0000000000..e5d81aa6bf
--- /dev/null
+++ b/browser_tests/tests/appModeInputPersistence.spec.ts
@@ -0,0 +1,44 @@
+import {
+  comfyPageFixture as test,
+  comfyExpect as expect
+} from '@e2e/fixtures/ComfyPage'
+import {
+  saveCloseAndReopenInBuilder,
+  setupBuilder
+} from '@e2e/fixtures/utils/builderTestUtils'
+
+const WIDGETS = ['seed', 'steps', 'cfg']
+
+test.describe(
+  'App builder input persistence after reload',
+  { tag: '@ui' },
+  () => {
+    test.beforeEach(async ({ comfyPage }) => {
+      await comfyPage.appMode.enableLinearMode()
+      await comfyPage.settings.setSetting(
+        'Comfy.AppBuilder.VueNodeSwitchDismissed',
+        true
+      )
+    })
+
+    test('persists selected inputs after save and reopen without visibility errors', async ({
+      comfyPage
+    }) => {
+      const { appMode } = comfyPage
+      await setupBuilder(comfyPage, undefined, WIDGETS)
+
+      await appMode.steps.goToInputs()
+      await expect(appMode.select.inputItemTitles).toHaveText(WIDGETS)
+
+      const workflowName = `${Date.now()} input-persistence`
+      await saveCloseAndReopenInBuilder(comfyPage, appMode, workflowName)
+
+      await expect(appMode.select.inputItemTitles).toHaveText(WIDGETS)
+      for (const widget of WIDGETS) {
+        await expect(
+          appMode.select.getInputItemSubtitle(widget)
+        ).not.toContainText('Widget not visible')
+      }
+    })
+  }
+)
diff --git a/browser_tests/tests/builderReorder.spec.ts b/browser_tests/tests/builderReorder.spec.ts
index feb73e7e74..27d5e54cb8 100644
--- a/browser_tests/tests/builderReorder.spec.ts
+++ b/browser_tests/tests/builderReorder.spec.ts
@@ -5,26 +5,18 @@ import {
 import type { AppModeHelper } from '@e2e/fixtures/helpers/AppModeHelper'
 import type { ComfyPage } from '@e2e/fixtures/ComfyPage'
 import {
-  builderSaveAs,
-  openWorkflowFromSidebar,
+  saveCloseAndReopenInBuilder,
   setupBuilder
 } from '@e2e/fixtures/utils/builderTestUtils'
 
 const WIDGETS = ['seed', 'steps', 'cfg']
 
-/** Save as app, close it by loading default, reopen from sidebar, enter app mode. */
 async function saveCloseAndReopenAsApp(
   comfyPage: ComfyPage,
   appMode: AppModeHelper,
   workflowName: string
 ) {
-  await appMode.steps.goToPreview()
-  await builderSaveAs(appMode, workflowName)
-  await appMode.saveAs.closeButton.click()
-  await expect(appMode.saveAs.successDialog).toBeHidden()
-
-  await appMode.footer.exitBuilder()
-  await openWorkflowFromSidebar(comfyPage, workflowName)
+  await saveCloseAndReopenInBuilder(comfyPage, appMode, workflowName)
   await appMode.toggleAppMode()
 }
 
diff --git a/src/stores/appModeStore.test.ts b/src/stores/appModeStore.test.ts
index d3a22987fc..1d64bbaa08 100644
--- a/src/stores/appModeStore.test.ts
+++ b/src/stores/appModeStore.test.ts
@@ -5,11 +5,16 @@ import { nextTick } from 'vue'
 import { beforeEach, describe, expect, it, vi } from 'vitest'
 
 import type { LGraphNode, NodeId } from '@/lib/litegraph/src/LGraphNode'
-import type { LoadedComfyWorkflow } from '@/platform/workflow/management/stores/comfyWorkflow'
+import type { IBaseWidget } from '@/lib/litegraph/src/types/widgets'
+import type {
+  InputWidgetConfig,
+  LinearInput,
+  LoadedComfyWorkflow
+} from '@/platform/workflow/management/stores/comfyWorkflow'
 import { ComfyWorkflow as ComfyWorkflowClass } from '@/platform/workflow/management/stores/comfyWorkflow'
 import { useWorkflowStore } from '@/platform/workflow/management/stores/workflowStore'
 import { app } from '@/scripts/app'
-import type { ChangeTracker } from '@/scripts/changeTracker'
+import { ChangeTracker } from '@/scripts/changeTracker'
 import { createMockChangeTracker } from '@/utils/__tests__/litegraphTestUtils'
 
 const mockEmptyWorkflowDialog = vi.hoisted(() => {
@@ -100,6 +105,29 @@ function createBuilderWorkflowWithOutputs(
   return workflow
 }
 
+function createWorkflowWithLinearData(
+  activeMode: string,
+  inputs: LinearInput[],
+  outputs: NodeId[]
+): LoadedComfyWorkflow {
+  const workflow = createBuilderWorkflow(activeMode)
+  workflow.changeTracker = createMockChangeTracker(
+    fromPartial<Partial<ChangeTracker>>({
+      activeState: {
+        last_node_id: 0,
+        last_link_id: 0,
+        nodes: [],
+        links: [],
+        groups: [],
+        config: {},
+        version: 0.4,
+        extra: { linearData: fromAny({ inputs, outputs }) }
+      }
+    })
+  )
+  return workflow
+}
+
 describe('appModeStore', () => {
   let workflowStore: ReturnType<typeof useWorkflowStore>
   let store: ReturnType<typeof useAppModeStore>
@@ -107,6 +135,7 @@ describe('appModeStore', () => {
   beforeEach(() => {
     setActivePinia(createTestingPinia({ stubActions: false }))
     vi.mocked(app.rootGraph).extra = {}
+    ChangeTracker.isLoadingGraph = false
     mockResolveNode.mockReturnValue(undefined)
     mockSettings.reset()
     vi.mocked(app.rootGraph).nodes = [{ id: 1 } as LGraphNode]
@@ -163,6 +192,28 @@ describe('appModeStore', () => {
       )
       expect(workflowStore.activeWorkflow!.activeMode).toBe('graph')
     })
+
+    it('prunes selections from workflow state on entry', () => {
+      const node1 = { id: 1 }
+      mockResolveNode.mockImplementation((id) =>
+        id == 1 ? fromAny<LGraphNode, unknown>(node1) : undefined
+      )
+      workflowStore.activeWorkflow = createWorkflowWithLinearData(
+        'graph',
+        [
+          [1, 'seed'],
+          [99, 'steps']
+        ],
+        [1, 99]
+      )
+      store.selectedInputs = [[42, 'prompt']]
+      store.selectedOutputs = [42]
+
+      store.enterBuilder()
+
+      expect(store.selectedInputs).toEqual([[1, 'seed']])
+      expect(store.selectedOutputs).toEqual([1])
+    })
   })
 
   describe('empty workflow dialog callbacks', () => {
@@ -202,33 +253,36 @@ describe('appModeStore', () => {
     })
   })
 
+  describe('exitBuilder', () => {
+    it('prunes selections from workflow state on exit', () => {
+      const node1 = { id: 1 }
+      mockResolveNode.mockImplementation((id) =>
+        id == 1 ? fromAny<LGraphNode, unknown>(node1) : undefined
+      )
+      workflowStore.activeWorkflow = createWorkflowWithLinearData(
+        'builder:inputs',
+        [
+          [1, 'seed'],
+          [99, 'steps']
+        ],
+        [1, 99]
+      )
+      store.selectedInputs = [[42, 'prompt']]
+      store.selectedOutputs = [42]
+
+      store.exitBuilder()
+
+      expect(store.selectedInputs).toEqual([[1, 'seed']])
+      expect(store.selectedOutputs).toEqual([1])
+      expect(workflowStore.activeWorkflow!.activeMode).toBe('graph')
+    })
+  })
+
   describe('loadSelections pruning', () => {
     function mockNode(id: number) {
       return { id }
     }
 
-    function workflowWithLinearData(
-      inputs: [number, string][],
-      outputs: number[]
-    ) {
-      const workflow = createBuilderWorkflow('app')
-      workflow.changeTracker = createMockChangeTracker(
-        fromPartial<Partial<ChangeTracker>>({
-          activeState: {
-            last_node_id: 0,
-            last_link_id: 0,
-            nodes: [],
-            links: [],
-            groups: [],
-            config: {},
-            version: 0.4,
-            extra: { linearData: { inputs, outputs } }
-          }
-        })
-      )
-      return workflow
-    }
-
     it('removes inputs referencing deleted nodes on load', async () => {
       const node1 = mockNode(1)
       mockResolveNode.mockImplementation((id) =>
@@ -294,7 +348,11 @@ describe('appModeStore', () => {
       // Initially nodes are not resolvable — pruning removes them
       mockResolveNode.mockReturnValue(undefined)
       const inputs: [number, string][] = [[1, 'seed']]
-      workflowStore.activeWorkflow = workflowWithLinearData(inputs, [1])
+      workflowStore.activeWorkflow = createWorkflowWithLinearData(
+        'app',
+        inputs,
+        [1]
+      )
       store.loadSelections({ inputs })
       await nextTick()
 
@@ -324,6 +382,141 @@ describe('appModeStore', () => {
     })
   })
 
+  describe('loadSelections edge cases', () => {
+    it('clears existing selections on undefined or empty data', () => {
+      store.selectedInputs = [[1, 'seed']]
+      store.selectedOutputs = [1]
+
+      store.loadSelections(undefined)
+
+      expect(store.selectedInputs).toEqual([])
+      expect(store.selectedOutputs).toEqual([])
+
+      store.selectedInputs = [[1, 'seed']]
+      store.selectedOutputs = [1]
+
+      store.loadSelections({})
+
+      expect(store.selectedInputs).toEqual([])
+      expect(store.selectedOutputs).toEqual([])
+    })
+  })
+
+  describe('pruneLinearData', () => {
+    it('returns empty selections for undefined data', () => {
+      expect(store.pruneLinearData(undefined)).toEqual({
+        inputs: [],
+        outputs: []
+      })
+    })
+
+    it('does not prune when rootGraph is empty', () => {
+      const originalRootGraph = app.rootGraph
+      Object.defineProperty(app, 'rootGraph', { value: null, writable: true })
+
+      try {
+        expect(
+          store.pruneLinearData({
+            inputs: [[1, 'seed']],
+            outputs: [1]
+          })
+        ).toEqual({
+          inputs: [[1, 'seed']],
+          outputs: [1]
+        })
+      } finally {
+        Object.defineProperty(app, 'rootGraph', {
+          value: originalRootGraph,
+          writable: true
+        })
+      }
+    })
+  })
+
+  describe('pruneLinearData during graph loading', () => {
+    it('preserves all entries when ChangeTracker.isLoadingGraph is true', () => {
+      ChangeTracker.isLoadingGraph = true
+
+      store.loadSelections({
+        inputs: [
+          [1, 'seed'],
+          [999, 'steps']
+        ],
+        outputs: [1, 999]
+      })
+
+      expect(store.selectedInputs).toEqual([
+        [1, 'seed'],
+        [999, 'steps']
+      ])
+      expect(store.selectedOutputs).toEqual([1, 999])
+    })
+
+    it('prunes entries for deleted nodes when not loading', () => {
+      const node1 = { id: 1 }
+      mockResolveNode.mockImplementation((id) =>
+        id == 1 ? fromAny<LGraphNode, unknown>(node1) : undefined
+      )
+
+      store.loadSelections({
+        inputs: [
+          [1, 'seed'],
+          [999, 'steps']
+        ],
+        outputs: [1, 999]
+      })
+
+      expect(store.selectedInputs).toEqual([[1, 'seed']])
+      expect(store.selectedOutputs).toEqual([1])
+    })
+  })
+
+  describe('resetSelectedToWorkflow fallback', () => {
+    it('falls back to initialState when activeState has no linearData', () => {
+      const node1 = { id: 1 }
+      mockResolveNode.mockImplementation((id) =>
+        id == 1 ? fromAny<LGraphNode, unknown>(node1) : undefined
+      )
+      const workflow = createBuilderWorkflow('app')
+      workflow.changeTracker.activeState.extra = {}
+      workflow.changeTracker.initialState = fromAny({
+        ...workflow.changeTracker.activeState,
+        extra: {
+          linearData: { inputs: [[1, 'seed']], outputs: [1] }
+        }
+      })
+      workflowStore.activeWorkflow = workflow
+
+      store.resetSelectedToWorkflow()
+
+      expect(store.selectedInputs).toEqual([[1, 'seed']])
+      expect(store.selectedOutputs).toEqual([1])
+    })
+
+    it('prefers activeState linearData when available', () => {
+      const node1 = { id: 1 }
+      mockResolveNode.mockImplementation((id) =>
+        id == 1 ? fromAny<LGraphNode, unknown>(node1) : undefined
+      )
+      const workflow = createBuilderWorkflow('app')
+      workflow.changeTracker.activeState.extra = {
+        linearData: { inputs: [[1, 'steps']], outputs: [1] }
+      }
+      workflow.changeTracker.initialState = fromAny({
+        ...workflow.changeTracker.activeState,
+        extra: {
+          linearData: { inputs: [[1, 'seed']], outputs: [1] }
+        }
+      })
+      workflowStore.activeWorkflow = workflow
+
+      store.resetSelectedToWorkflow()
+
+      expect(store.selectedInputs).toEqual([[1, 'steps']])
+      expect(store.selectedOutputs).toEqual([1])
+    })
+  })
+
   describe('linearData sync watcher', () => {
     it('writes linearData to rootGraph.extra when in builder mode', async () => {
       workflowStore.activeWorkflow = createBuilderWorkflow()
@@ -353,15 +546,22 @@ describe('appModeStore', () => {
       await nextTick()
 
       const originalRootGraph = app.rootGraph
+      const dataBefore = JSON.parse(
+        JSON.stringify(originalRootGraph.extra.linearData)
+      )
       Object.defineProperty(app, 'rootGraph', { value: null, writable: true })
 
-      store.selectedOutputs.push(1)
-      await nextTick()
+      try {
+        store.selectedOutputs.push(1)
+        await nextTick()
+      } finally {
+        Object.defineProperty(app, 'rootGraph', {
+          value: originalRootGraph,
+          writable: true
+        })
+      }
 
-      Object.defineProperty(app, 'rootGraph', {
-        value: originalRootGraph,
-        writable: true
-      })
+      expect(originalRootGraph.extra.linearData).toEqual(dataBefore)
     })
 
     it('calls captureCanvasState when input is selected', async () => {
@@ -428,6 +628,18 @@ describe('appModeStore', () => {
       expect(store.selectedInputs[0][2]).toEqual({ height: 200 })
     })
 
+    it('merges existing config with new values', () => {
+      const existingConfig: InputWidgetConfig & { width: number } = {
+        height: 120,
+        width: 240
+      }
+      store.selectedInputs.push([1, 'prompt', existingConfig])
+
+      store.updateInputConfig(1 as NodeId, 'prompt', { height: 300 })
+
+      expect(store.selectedInputs[0][2]).toEqual({ height: 300, width: 240 })
+    })
+
     it('triggers linearData sync watcher', async () => {
       workflowStore.activeWorkflow = createBuilderWorkflow()
       store.selectedInputs.push([42, 'prompt'])
@@ -443,6 +655,17 @@ describe('appModeStore', () => {
     })
   })
 
+  describe('removeSelectedInput', () => {
+    it('removes the matching input entry only', () => {
+      store.selectedInputs.push([1, 'prompt'])
+      store.selectedInputs.push([2, 'steps'])
+
+      store.removeSelectedInput({ name: 'steps' } as IBaseWidget, { id: 2 })
+
+      expect(store.selectedInputs).toEqual([[1, 'prompt']])
+    })
+  })
+
   describe('autoEnableVueNodes', () => {
     it('enables Vue nodes when entering select mode with them disabled', async () => {
       mockSettings.store['Comfy.VueNodes.Enabled'] = false
diff --git a/src/stores/appModeStore.ts b/src/stores/appModeStore.ts
index 56a648d1f7..307049246f 100644
--- a/src/stores/appModeStore.ts
+++ b/src/stores/appModeStore.ts
@@ -49,14 +49,13 @@ export const useAppModeStore = defineStore('appMode', () => {
   function pruneLinearData(data: Partial<LinearData> | undefined): LinearData {
     const rawInputs = data?.inputs ?? []
     const rawOutputs = data?.outputs ?? []
+    if (!app.rootGraph || ChangeTracker.isLoadingGraph) {
+      return { inputs: rawInputs, outputs: rawOutputs }
+    }
 
     return {
-      inputs: app.rootGraph
-        ? rawInputs.filter(([nodeId]) => resolveNode(nodeId))
-        : rawInputs,
-      outputs: app.rootGraph
-        ? rawOutputs.filter((nodeId) => resolveNode(nodeId))
-        : rawOutputs
+      inputs: rawInputs.filter(([nodeId]) => resolveNode(nodeId)),
+      outputs: rawOutputs.filter((nodeId) => resolveNode(nodeId))
     }
   }
 
@@ -70,7 +69,10 @@ export const useAppModeStore = defineStore('appMode', () => {
     const { activeWorkflow } = workflowStore
     if (!activeWorkflow) return
 
-    loadSelections(activeWorkflow.changeTracker?.activeState?.extra?.linearData)
+    const source =
+      activeWorkflow.changeTracker?.activeState?.extra?.linearData ??
+      activeWorkflow.initialState?.extra?.linearData
+    loadSelections(source)
   }
 
   useEventListener(