diff --git a/packages/server/src/enterprise/controllers/auth/index.ts b/packages/server/src/enterprise/controllers/auth/index.ts
index bf1c742e99b..8fae291c1a5 100644
--- a/packages/server/src/enterprise/controllers/auth/index.ts
+++ b/packages/server/src/enterprise/controllers/auth/index.ts
@@ -11,6 +11,10 @@ const getAllPermissions = async (req: Request, res: Response, next: NextFunction
         const allPermissions = appServer.identityManager.getPermissions().toJSON()
         const user = req.user as LoggedInUser
 
+        if (!user) {
+            return res.status(StatusCodes.UNAUTHORIZED).json({ message: 'Unauthorized' })
+        }
+
         let permissions: { [key: string]: { key: string; value: string }[] } = allPermissions
 
         // Mapping of feature flags to permission prefixes
diff --git a/packages/server/src/utils/buildChatflow.ts b/packages/server/src/utils/buildChatflow.ts
index c54c009c43a..02cd62ab205 100644
--- a/packages/server/src/utils/buildChatflow.ts
+++ b/packages/server/src/utils/buildChatflow.ts
@@ -448,7 +448,7 @@ export const executeFlow = async ({
             if (fileInputFieldFromExt !== 'txtFile') {
                 fileInputField = fileInputFieldFromExt
             } else if (fileInputFieldFromMimeType !== 'txtFile') {
-                fileInputField = fileInputFieldFromExt
+                fileInputField = fileInputFieldFromMimeType
             }
 
             if (overrideConfig[fileInputField]) {
diff --git a/packages/server/src/utils/index.ts b/packages/server/src/utils/index.ts
index 7ea3adbfd8e..9158d66cb77 100644
--- a/packages/server/src/utils/index.ts
+++ b/packages/server/src/utils/index.ts
@@ -1187,9 +1187,17 @@ export const replaceInputsWithConfig = (
                     continue
                 }
             } else {
+                // For FILE-STORAGE:: values (uploaded files mapped to txtFile, pdfFile, etc.),
+                // also allow override if the generic 'file' parameter is enabled for the node.
+                // This handles the case where users enable the 'file' input for override in the UI,
+                // which should also permit the server-side file-type fields to be applied.
+                const isFileStorageValue =
+                    typeof overrideConfig[config] === 'string' && overrideConfig[config].includes('FILE-STORAGE::')
                 if (!isParameterEnabled(flowNodeData.label, config)) {
-                    // Only proceed if the parameter is enabled
-                    continue
+                    if (!(isFileStorageValue && isParameterEnabled(flowNodeData.label, 'file'))) {
+                        // Only proceed if the parameter is enabled
+                        continue
+                    }
                 }
             }
 
diff --git a/packages/server/src/utils/upsertVector.ts b/packages/server/src/utils/upsertVector.ts
index b7c17b45dcf..04e26e3bdf8 100644
--- a/packages/server/src/utils/upsertVector.ts
+++ b/packages/server/src/utils/upsertVector.ts
@@ -96,7 +96,7 @@ export const executeUpsert = async ({
             if (fileInputFieldFromExt !== 'txtFile') {
                 fileInputField = fileInputFieldFromExt
             } else if (fileInputFieldFromMimeType !== 'txtFile') {
-                fileInputField = fileInputFieldFromExt
+                fileInputField = fileInputFieldFromMimeType
             }
 
             if (overrideConfig[fileInputField]) {