OneDrive for Business file server migration misses files for finance folders: Fix Guide

Your finance team completed a file server migration to OneDrive for Business, but some files are missing from the finance folders. This problem occurs when the migration tool skips files due to permission errors, file name length limits, or unsupported characters in file paths. This article explains the root causes of missing files during migration and provides step-by-step fixes to locate and restore the missing data.

Why OneDrive File Server Migration Misses Files in Finance Folders

The SharePoint Migration Tool (SPMT) and Mover.io both scan the source file server and copy files to OneDrive. The migration engine logs a success or failure for each file. Files are skipped silently or logged as failures when any of these conditions occur:

Finance folders often contain deeply nested subfolders, long file names with dates and version numbers, and files with special characters such as &, #, %, and +. The migration tool treats these characters as unsupported in SharePoint Online and OneDrive. Additionally, the service account used for migration must have NTFS Read permissions on every folder and file in the finance directory tree. If a single subfolder has explicit Deny entries or missing inherited permissions, the tool skips all files under that folder.

Another common cause is file type blocking at the tenant level. The OneDrive admin center can block file extensions such as .exe, .ps1, and .vbs. Finance teams sometimes store script files or macro-enabled Excel workbooks (.xlsm) that get blocked. The migration tool reports these as failures, not as missing files.

Step-by-Step Fixes to Locate and Restore Missing Finance Files

Step 1: Export the Migration Error Report

1. Open the SharePoint Migration Tool
   Launch SPMT on the machine that ran the migration. If you used Mover.io, log in to the Mover dashboard and select the completed migration job.
2. Locate the job summary
   In SPMT, click the job name. On the job details page, click View Report. In Mover.io, click View Logs on the completed transfer.
3. Export the report to CSV
   In SPMT, click Export to CSV. In Mover.io, click Download CSV. Save the file to a local folder.

Step 2: Filter the CSV for Finance Folders and Failure Reasons

1. Open the CSV in Excel
   Double-click the exported CSV file. It opens in Excel. If prompted, set the delimiter to comma.
2. Filter by source path
   Select the entire table. On the Data tab, click Filter. Click the filter arrow on the Source Path column. Type Finance in the search box. Select only rows that contain “Finance”.
3. Identify failure reasons
   Look at the Status column. Filter for values that contain “Failed”, “Skipped”, or “Warning”. The Error Message column shows the exact reason: “Path too long”, “Access denied”, “Unsupported file type”, or “Invalid character”.

Step 3: Fix Path Too Long Errors

1. Shorten the folder names on the source server
   Rename the deepest folders to use fewer characters. For example, rename “2024_Q4_Finance_Consolidated_Reports” to “Q4_Fin_Rpts”. After renaming, re-run the migration for only the affected folder.
2. Use the SPMT long path flag
   In SPMT, when creating a new task, check the box Enable support for long file paths under Advanced settings. This allows paths up to 400 characters.

Step 4: Fix Access Denied Errors

1. Check NTFS permissions on the source server
   Right-click the Finance root folder on the file server. Select Properties > Security tab. Click Advanced. Verify that the service account used for migration has Read & Execute and List folder contents permissions. If the account is missing, click Add and grant those permissions.
2. Remove explicit Deny entries
   In the same Advanced Security Settings window, look for any Deny entries that affect the service account or the Finance group. If a Deny entry exists, select it and click Remove. Only remove Deny entries if they are not required for security policy.
3. Re-run the migration for the affected folder
   In SPMT, create a new task. Select only the Finance folder as the source. The tool will scan again and copy previously skipped files.

Step 5: Fix Unsupported File Types

1. Check the blocked file types list
   Go to the Microsoft 365 admin center. Select Settings > Org settings > OneDrive. Under Sync, look for Block syncing of specific file types. If the missing file extension is listed, remove it from the blocked list.
2. Zip the blocked files before migration
   On the source server, select all files with blocked extensions. Right-click and choose Send to > Compressed (zipped) folder. Move the zip file to a folder that is not blocked. Then re-run the migration.

Step 6: Fix Invalid Character Errors

1. Rename files on the source server
   In File Explorer, navigate to the source Finance folder. Locate files with characters like &, #, %, +, or curly braces. Rename each file to remove those characters. Replace & with “and”. Replace # with “num”.
2. Re-run the migration for the renamed files
   After renaming, run SPMT again. Select only the folders that contained renamed files.

If OneDrive Still Has Missing Files After the Main Fix

OneDrive shows a red X on shared finance files

When a file is missing from OneDrive but still exists on the file server, the migration might have skipped it because of a sync conflict. Open the OneDrive activity center by clicking the OneDrive cloud icon in the system tray. Look for Sync conflicts or Files that couldn’t be synced. Click Resolve and choose Keep both to restore the server version to OneDrive.

Finance subfolders appear empty in OneDrive but not on the server

This usually happens when the migration tool copied the folder structure but failed to copy contents due to a file-level permission error. Compare the folder list in OneDrive with the source server. For each empty folder, go back to Step 4 and verify permissions on the source folder. Then re-run the migration for that specific folder.

SPMT vs Mover.io: Migration Tool Comparison for Finance Folders

Item	SPMT (SharePoint Migration Tool)	Mover.io
Supported sources	Windows file servers, SharePoint on-premises	File servers, Box, Dropbox, Google Drive, and 20+ other cloud providers
Long path support	Up to 400 characters with flag enabled	Up to 256 characters; no long path flag
Error report granularity	Per-file CSV with error code and message	Per-file CSV with status and reason
Unsupported character handling	Automatically replaces &, #, % with underscore	Fails on &, #, %; requires manual rename
Permission migration	Copies NTFS permissions to SharePoint groups	Does not copy permissions; requires manual setup

After completing the fixes, you can now open OneDrive and confirm that all finance files appear in the correct folders. Next, run a manual comparison using a script or tool like TreeSize to verify that the file count matches between the source server and OneDrive. An advanced tip: schedule a delta migration pass using SPMT’s incremental scan to catch any files that were added or changed after the initial migration.