diff --git a/src/platform/workflow/core/services/workflowService.ts b/src/platform/workflow/core/services/workflowService.ts
index 10bbee0d3c..3660e66842 100644
--- a/src/platform/workflow/core/services/workflowService.ts
+++ b/src/platform/workflow/core/services/workflowService.ts
@@ -21,6 +21,7 @@ import { useDialogService } from '@/services/dialogService'
 import { useAppMode } from '@/composables/useAppMode'
 import type { AppMode } from '@/composables/useAppMode'
 import { useDomWidgetStore } from '@/stores/domWidgetStore'
+import { useAppModeStore } from '@/stores/appModeStore'
 import { useExecutionErrorStore } from '@/stores/executionErrorStore'
 import { useWorkspaceStore } from '@/stores/workspaceStore'
 import {
@@ -404,6 +405,7 @@ export const useWorkflowService = () => {
     // Determine the initial app mode for fresh loads from serialized state.
     // null means linearMode was never explicitly set (not builder-saved).
     const freshLoadMode = linearModeToAppMode(workflowData.extra?.linearMode)
+    useAppModeStore().loadSelections(workflowData.extra?.linearData)
 
     function trackIfEnteringApp(workflow: ComfyWorkflow) {
       if (!wasAppMode && workflow.initialMode === 'app') {
diff --git a/src/stores/appModeStore.test.ts b/src/stores/appModeStore.test.ts
index c8d4d3e661..ae900db5d3 100644
--- a/src/stores/appModeStore.test.ts
+++ b/src/stores/appModeStore.test.ts
@@ -197,14 +197,12 @@ describe('appModeStore', () => {
         id == 1 ? (node1 as unknown as LGraphNode) : undefined
       )
 
-      workflowStore.activeWorkflow = workflowWithLinearData(
-        [
+      store.loadSelections({
+        inputs: [
           [1, 'prompt'],
           [99, 'width']
-        ],
-        []
-      )
-      await nextTick()
+        ]
+      })
 
       expect(store.selectedInputs).toEqual([[1, 'prompt']])
     })
@@ -215,14 +213,12 @@ describe('appModeStore', () => {
         id == 1 ? (node1 as unknown as LGraphNode) : undefined
       )
 
-      workflowStore.activeWorkflow = workflowWithLinearData(
-        [
+      store.loadSelections({
+        inputs: [
           [1, 'prompt'],
           [1, 'deleted_widget']
-        ],
-        []
-      )
-      await nextTick()
+        ]
+      })
 
       expect(store.selectedInputs).toEqual([
         [1, 'prompt'],
@@ -236,8 +232,7 @@ describe('appModeStore', () => {
         id == 1 ? (node1 as unknown as LGraphNode) : undefined
       )
 
-      workflowStore.activeWorkflow = workflowWithLinearData([], [1, 99])
-      await nextTick()
+      store.loadSelections({ outputs: [1, 99] })
 
       expect(store.selectedOutputs).toEqual([1])
     })
@@ -247,8 +242,11 @@ describe('appModeStore', () => {
 
       // Initially nodes are not resolvable — pruning removes them
       mockResolveNode.mockReturnValue(undefined)
-      workflowStore.activeWorkflow = workflowWithLinearData([[1, 'seed']], [1])
+      const inputs: [number, string][] = [[1, 'seed']]
+      workflowStore.activeWorkflow = workflowWithLinearData(inputs, [1])
+      store.loadSelections({ inputs })
       await nextTick()
+
       expect(store.selectedInputs).toEqual([])
       expect(store.selectedOutputs).toEqual([])
 
@@ -268,8 +266,7 @@ describe('appModeStore', () => {
     it('hasOutputs is false when all output nodes are deleted', async () => {
       mockResolveNode.mockReturnValue(undefined)
 
-      workflowStore.activeWorkflow = workflowWithLinearData([], [10, 20])
-      await nextTick()
+      store.loadSelections({ outputs: [10, 20] })
 
       expect(store.selectedOutputs).toEqual([])
       expect(store.hasOutputs).toBe(false)
diff --git a/src/stores/appModeStore.ts b/src/stores/appModeStore.ts
index 75603e9c37..edc8f04a0d 100644
--- a/src/stores/appModeStore.ts
+++ b/src/stores/appModeStore.ts
@@ -1,5 +1,5 @@
 import { defineStore } from 'pinia'
-import { reactive, computed, watch } from 'vue'
+import { ref, computed, watch } from 'vue'
 import { useEventListener } from '@vueuse/core'
 
 import { useEmptyWorkflowDialog } from '@/components/builder/useEmptyWorkflowDialog'
@@ -25,9 +25,9 @@ export const useAppModeStore = defineStore('appMode', () => {
   const { mode, setMode, isBuilderMode, isSelectMode } = useAppMode()
   const emptyWorkflowDialog = useEmptyWorkflowDialog()
 
-  const selectedInputs = reactive<[NodeId, string][]>([])
-  const selectedOutputs = reactive<NodeId[]>([])
-  const hasOutputs = computed(() => !!selectedOutputs.length)
+  const selectedInputs = ref<[NodeId, string][]>([])
+  const selectedOutputs = ref<NodeId[]>([])
+  const hasOutputs = computed(() => !!selectedOutputs.value.length)
   const hasNodes = computed(() => {
     // Nodes are not reactive, so trigger recomputation when workflow changes
     void workflowStore.activeWorkflow
@@ -54,8 +54,8 @@ export const useAppModeStore = defineStore('appMode', () => {
 
   function loadSelections(data: Partial<LinearData> | undefined) {
     const { inputs, outputs } = pruneLinearData(data)
-    selectedInputs.splice(0, selectedInputs.length, ...inputs)
-    selectedOutputs.splice(0, selectedOutputs.length, ...outputs)
+    selectedInputs.value = inputs
+    selectedOutputs.value = outputs
   }
 
   function resetSelectedToWorkflow() {
@@ -65,20 +65,6 @@ export const useAppModeStore = defineStore('appMode', () => {
     loadSelections(activeWorkflow.changeTracker?.activeState?.extra?.linearData)
   }
 
-  watch(
-    () => workflowStore.activeWorkflow,
-    (newWorkflow) => {
-      if (newWorkflow) {
-        loadSelections(
-          newWorkflow.changeTracker?.activeState?.extra?.linearData
-        )
-      } else {
-        loadSelections(undefined)
-      }
-    },
-    { immediate: true }
-  )
-
   useEventListener(
     () => app.rootGraph?.events,
     'configured',
@@ -88,7 +74,7 @@ export const useAppModeStore = defineStore('appMode', () => {
   watch(
     () =>
       isBuilderMode.value
-        ? { inputs: selectedInputs, outputs: selectedOutputs }
+        ? { inputs: selectedInputs.value, outputs: selectedOutputs.value }
         : null,
     (data) => {
       if (!data || ChangeTracker.isLoadingGraph) return
@@ -144,10 +130,10 @@ export const useAppModeStore = defineStore('appMode', () => {
     const storeName = isPromotedWidgetView(widget)
       ? widget.sourceWidgetName
       : widget.name
-    const index = selectedInputs.findIndex(
+    const index = selectedInputs.value.findIndex(
       ([id, name]) => storeId == id && storeName === name
     )
-    if (index !== -1) selectedInputs.splice(index, 1)
+    if (index !== -1) selectedInputs.value.splice(index, 1)
   }
 
   return {
@@ -155,6 +141,7 @@ export const useAppModeStore = defineStore('appMode', () => {
     exitBuilder,
     hasNodes,
     hasOutputs,
+    loadSelections,
     pruneLinearData,
     removeSelectedInput,
     resetSelectedToWorkflow,