diff --git a/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx b/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx
index 80de905352..f6bd486ea2 100644
--- a/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/node-menu.spec.tsx
@@ -26,8 +26,6 @@ type MockFileOperations = {
   handleDownload: () => void
   handleNewFile: () => void
   handleNewFolder: () => void
-  handleFileChange: () => void
-  handleFolderChange: () => void
   handleRename: () => void
   handleDeleteClick: () => void
   handleDeleteConfirm: () => void
@@ -53,8 +51,6 @@ function createFileOperationsMock(): MockFileOperations {
     handleDownload: vi.fn(),
     handleNewFile: vi.fn(),
     handleNewFolder: vi.fn(),
-    handleFileChange: vi.fn(),
-    handleFolderChange: vi.fn(),
     handleRename: vi.fn(),
     handleDeleteClick: vi.fn(),
     handleDeleteConfirm: vi.fn(),
@@ -106,8 +102,6 @@ const renderNodeMenu = ({
               onDownload={mocks.fileOperations.handleDownload}
               onNewFile={mocks.fileOperations.handleNewFile}
               onNewFolder={mocks.fileOperations.handleNewFolder}
-              onFileChange={mocks.fileOperations.handleFileChange}
-              onFolderChange={mocks.fileOperations.handleFolderChange}
               onRename={mocks.fileOperations.handleRename}
               onDeleteClick={mocks.fileOperations.handleDeleteClick}
               onImportSkills={onImportSkills}
@@ -131,8 +125,6 @@ const renderNodeMenu = ({
               onDownload={mocks.fileOperations.handleDownload}
               onNewFile={mocks.fileOperations.handleNewFile}
               onNewFolder={mocks.fileOperations.handleNewFolder}
-              onFileChange={mocks.fileOperations.handleFileChange}
-              onFolderChange={mocks.fileOperations.handleFolderChange}
               onRename={mocks.fileOperations.handleRename}
               onDeleteClick={mocks.fileOperations.handleDeleteClick}
               onImportSkills={onImportSkills}
@@ -205,13 +197,20 @@ describe('NodeMenu', () => {
     })
 
     it('should trigger hidden file and folder input clicks from upload actions', () => {
-      const clickSpy = vi.spyOn(HTMLInputElement.prototype, 'click')
+      const fileInput = document.createElement('input')
+      const folderInput = document.createElement('input')
+      const fileClickSpy = vi.spyOn(fileInput, 'click')
+      const folderClickSpy = vi.spyOn(folderInput, 'click')
+      mocks.fileOperations.fileInputRef.current = fileInput
+      mocks.fileOperations.folderInputRef.current = folderInput
+
       renderNodeMenu({ type: NODE_MENU_TYPE.FOLDER })
 
       fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.uploadFile/i }))
       fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.uploadFolder/i }))
 
-      expect(clickSpy).toHaveBeenCalledTimes(2)
+      expect(fileClickSpy).toHaveBeenCalledTimes(1)
+      expect(folderClickSpy).toHaveBeenCalledTimes(1)
     })
 
     it('should cut explicit action node ids and close menu when cut is clicked', () => {
diff --git a/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx b/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx
index 58295ef10d..b8b5b4a77b 100644
--- a/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/node-menu.tsx
@@ -32,8 +32,6 @@ type NodeMenuProps = {
   onDownload: () => void
   onNewFile: () => void
   onNewFolder: () => void
-  onFileChange: React.ChangeEventHandler<HTMLInputElement>
-  onFolderChange: React.ChangeEventHandler<HTMLInputElement>
   onRename: () => void
   onDeleteClick: () => void
   onImportSkills?: () => void
@@ -51,8 +49,6 @@ const NodeMenu = ({
   onDownload,
   onNewFile,
   onNewFolder,
-  onFileChange,
-  onFolderChange,
   onRename,
   onDeleteClick,
   onImportSkills,
@@ -97,24 +93,6 @@ const NodeMenu = ({
     <>
       {isFolder && (
         <>
-          <input
-            ref={fileInputRef}
-            type="file"
-            multiple
-            className="hidden"
-            aria-label={t('skillSidebar.menu.uploadFile')}
-            onChange={onFileChange}
-          />
-          <input
-            ref={folderInputRef}
-            type="file"
-            // @ts-expect-error webkitdirectory is a non-standard attribute
-            webkitdirectory=""
-            className="hidden"
-            aria-label={t('skillSidebar.menu.uploadFolder')}
-            onChange={onFolderChange}
-          />
-
           <MenuItem
             menuType={menuType}
             icon={FileAdd}
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
index f22a4f720e..15dd14ae0a 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
@@ -15,6 +15,7 @@ import { NODE_MENU_TYPE, ROOT_ID } from '../../constants'
 import { useFileOperations } from '../../hooks/file-tree/operations/use-file-operations'
 import NodeDeleteConfirmDialog from './node-delete-confirm-dialog'
 import NodeMenu from './node-menu'
+import UploadInputs from './upload-inputs'
 
 const ImportSkillModal = dynamic(() => import('../../start-tab/import-skill-modal'), {
   ssr: false,
@@ -106,6 +107,12 @@ const TreeContextMenu = ({
 
   return (
     <>
+      <UploadInputs
+        fileInputRef={fileOperations.fileInputRef}
+        folderInputRef={fileOperations.folderInputRef}
+        onFileChange={fileOperations.handleFileChange}
+        onFolderChange={fileOperations.handleFolderChange}
+      />
       <ContextMenu>
         <ContextMenuTrigger
           ref={triggerRef}
@@ -127,8 +134,6 @@ const TreeContextMenu = ({
             onDownload={fileOperations.handleDownload}
             onNewFile={fileOperations.handleNewFile}
             onNewFolder={fileOperations.handleNewFolder}
-            onFileChange={fileOperations.handleFileChange}
-            onFolderChange={fileOperations.handleFolderChange}
             onRename={fileOperations.handleRename}
             onDeleteClick={fileOperations.handleDeleteClick}
             onImportSkills={isRootTarget ? handleOpenImportSkills : undefined}
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
index c54da65dde..0494d2e47a 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
@@ -21,6 +21,7 @@ import NodeMenu from './node-menu'
 import TreeEditInput from './tree-edit-input'
 import TreeGuideLines from './tree-guide-lines'
 import { TreeNodeIcon } from './tree-node-icon'
+import UploadInputs from './upload-inputs'
 
 type TreeNodeProps = NodeRendererProps<TreeNodeData> & {
   treeChildren: TreeNodeData[]
@@ -101,6 +102,12 @@ const TreeNode = ({ node, style, dragHandle, treeChildren }: TreeNodeProps) => {
 
   return (
     <>
+      <UploadInputs
+        fileInputRef={fileOperations.fileInputRef}
+        folderInputRef={fileOperations.folderInputRef}
+        onFileChange={fileOperations.handleFileChange}
+        onFolderChange={fileOperations.handleFolderChange}
+      />
       <div
         ref={dragHandle}
         style={style}
@@ -195,8 +202,6 @@ const TreeNode = ({ node, style, dragHandle, treeChildren }: TreeNodeProps) => {
               onDownload={fileOperations.handleDownload}
               onNewFile={fileOperations.handleNewFile}
               onNewFolder={fileOperations.handleNewFolder}
-              onFileChange={fileOperations.handleFileChange}
-              onFolderChange={fileOperations.handleFolderChange}
               onRename={fileOperations.handleRename}
               onDeleteClick={fileOperations.handleDeleteClick}
             />
diff --git a/web/app/components/workflow/skill/file-tree/tree/upload-inputs.tsx b/web/app/components/workflow/skill/file-tree/tree/upload-inputs.tsx
new file mode 100644
index 0000000000..e09e434500
--- /dev/null
+++ b/web/app/components/workflow/skill/file-tree/tree/upload-inputs.tsx
@@ -0,0 +1,44 @@
+'use client'
+
+import * as React from 'react'
+import { useTranslation } from 'react-i18next'
+
+type UploadInputsProps = {
+  fileInputRef: React.RefObject<HTMLInputElement | null>
+  folderInputRef: React.RefObject<HTMLInputElement | null>
+  onFileChange: React.ChangeEventHandler<HTMLInputElement>
+  onFolderChange: React.ChangeEventHandler<HTMLInputElement>
+}
+
+const UploadInputs = ({
+  fileInputRef,
+  folderInputRef,
+  onFileChange,
+  onFolderChange,
+}: UploadInputsProps) => {
+  const { t } = useTranslation('workflow')
+
+  return (
+    <>
+      <input
+        ref={fileInputRef}
+        type="file"
+        multiple
+        className="hidden"
+        aria-label={t('skillSidebar.menu.uploadFile')}
+        onChange={onFileChange}
+      />
+      <input
+        ref={folderInputRef}
+        type="file"
+        // @ts-expect-error webkitdirectory is a non-standard attribute
+        webkitdirectory=""
+        className="hidden"
+        aria-label={t('skillSidebar.menu.uploadFolder')}
+        onChange={onFolderChange}
+      />
+    </>
+  )
+}
+
+export default React.memo(UploadInputs)
diff --git a/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx b/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx
index 30993e7229..756592db01 100644
--- a/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx
+++ b/web/app/components/workflow/skill/skill-body/sidebar-search-add.spec.tsx
@@ -162,6 +162,27 @@ describe('SidebarSearchAdd', () => {
       expect(clickSpy).toHaveBeenCalledTimes(2)
     })
 
+    it('should keep upload inputs mounted after menu closes so change handlers still run', () => {
+      // Arrange
+      render(<SidebarSearchAdd />)
+      fireEvent.click(screen.getByRole('button', { name: /common\.operation\.add/i }))
+
+      // Act
+      fireEvent.click(screen.getByRole('menuitem', { name: /workflow\.skillSidebar\.menu\.uploadFile/i }))
+
+      // Assert
+      const uploadFileInput = document.querySelector('input[type="file"][multiple]') as HTMLInputElement | null
+      expect(uploadFileInput).not.toBeNull()
+
+      fireEvent.change(uploadFileInput!, {
+        target: {
+          files: [new File(['content'], 'readme.md', { type: 'text/markdown' })],
+        },
+      })
+
+      expect(mocks.fileOperations.handleFileChange).toHaveBeenCalledTimes(1)
+    })
+
     it('should open and close import modal when import skills action is used', () => {
       // Arrange
       render(<SidebarSearchAdd />)
diff --git a/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx b/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx
index 8fc94093db..f1d29588c3 100644
--- a/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx
+++ b/web/app/components/workflow/skill/skill-body/sidebar-search-add.tsx
@@ -18,6 +18,7 @@ import dynamic from '@/next/dynamic'
 import { cn } from '@/utils/classnames'
 import { ROOT_ID } from '../constants'
 import MenuItem from '../file-tree/tree/menu-item'
+import UploadInputs from '../file-tree/tree/upload-inputs'
 import { useSkillAssetTreeData } from '../hooks/file-tree/data/use-skill-asset-tree'
 import { useFileOperations } from '../hooks/file-tree/operations/use-file-operations'
 import { getTargetFolderIdFromSelection } from '../utils/tree-utils'
@@ -69,6 +70,12 @@ const SidebarSearchAdd = () => {
 
   return (
     <div className="flex items-center gap-1 p-2">
+      <UploadInputs
+        fileInputRef={fileInputRef}
+        folderInputRef={folderInputRef}
+        onFileChange={handleFileChange}
+        onFolderChange={handleFolderChange}
+      />
       <SearchInput
         value={searchValue}
         onChange={v => storeApi.getState().setFileTreeSearchTerm(v)}
@@ -91,22 +98,6 @@ const SidebarSearchAdd = () => {
           sideOffset={4}
           popupClassName="min-w-[180px]"
         >
-          <input
-            ref={fileInputRef}
-            type="file"
-            multiple
-            className="hidden"
-            onChange={handleFileChange}
-          />
-          <input
-            ref={folderInputRef}
-            type="file"
-            // @ts-expect-error webkitdirectory is a non-standard attribute
-            webkitdirectory=""
-            className="hidden"
-            onChange={handleFolderChange}
-          />
-
           <MenuItem
             menuType="dropdown"
             icon={FileAdd}