OneDrive for Business file server migration misses files for weekend cutovers: Fix Guide

When migrating file server data to OneDrive for Business over a weekend cutover, some files commonly do not appear in the target OneDrive libraries after the migration completes. This problem occurs because the initial sync or migration tool finishes scanning the source before all weekend changes are written to disk, leaving the final edits, new files, and metadata updates stranded on the source server. This article explains why files get missed during weekend cutovers and provides the exact steps to locate and migrate those missing items without restarting the entire migration.

Why Weekend Cutovers Cause Missing Files in OneDrive Migrations

File server migrations to OneDrive for Business typically use a multi-pass approach: an initial full scan, one or more delta scans, and a final cutover scan. The migration tool, such as the SharePoint Migration Tool SPMT, scans the source file server at a point in time. If users, automated scripts, or backup processes write files after the final scan begins, those files are never included in the migration package.

Weekend cutovers are especially vulnerable because the migration team often starts the final scan Friday evening and expects it to finish by Sunday night. However, scheduled tasks, database dumps, or antivirus scans can write files during the weekend that the migration tool does not see. The tool reports success because it scanned the folder structure and found no changes after its internal timestamp cutoff, but the new files exist on disk.

The Role of File Locking and Open Handles

Another common cause is file locking. If a file is open by a user or a service during the migration scan, the tool skips it or reports it as locked. After the cutover, the file remains on the source server and never appears in OneDrive. The migration log shows a warning for that file, but the overall job status may still show as completed.

Folder Redirection and Known Folder Move Conflicts

When the migration includes folders that are redirected by Group Policy, such as Desktop or Documents, the migration tool may interpret the redirected path as a junction point and skip the actual content. This results in empty folders in OneDrive while the files remain on the file server.

Steps to Find and Migrate the Missing Files After a Weekend Cutover

Do not restart the entire migration. Instead, run a delta pass that targets only the files that were missed. The following steps assume you used the SharePoint Migration Tool SPMT, but the logic applies to any migration tool that supports incremental scanning.

1. Identify the missing files on the source file server
   Open File Explorer on the source server. Navigate to the root folder that was migrated. Right-click the folder and select Properties. Go to the Previous Versions tab. Look for any files or folders that have a version timestamp after the time your final migration scan started. Alternatively, use PowerShell: Get-ChildItem -Path "\\Server\Share" -Recurse | Where-Object {$_.LastWriteTime -gt "2025-03-28 18:00:00"} | Export-Csv C:\Temp\missingfiles.csv. Replace the path and timestamp with your actual source and cutover start time.
2. Check the SPMT migration report for skipped items
   Open SPMT. Go to the Reports tab. Find the job that ran during the cutover. Click View Report. Look for rows where the Status column shows Skipped or Failed. Export that list to CSV. Cross-reference the file paths with the missing files list from step 1.
3. Run a delta pass in SPMT with the same source and destination
   In SPMT, click Add a new task. Select the same source path that was used in the original migration. For the destination, enter the same OneDrive library URL. Under Advanced Settings, enable Scan only new and modified files. Set the scan timeout to 60 minutes to allow the tool to recheck all files. Start the task. SPMT will compare the source files against the destination and upload only the files that are missing or have a newer timestamp.
4. Verify file permissions and metadata after the delta pass
   After the delta pass completes, open the OneDrive library in a browser. Select a few files from the missing list. Click the information icon. Confirm that the Modified date matches the source file. Check the Sharing settings to ensure permissions from the source file server were applied. If permissions are missing, use the Set-SPOTenantSyncPolicy PowerShell cmdlet to reapply them.
5. Delete the original migration package to avoid duplicates
   If the delta pass created duplicate files with a suffix like _1.docx, go to the OneDrive library. Switch to the Activity view. Look for files uploaded during the delta pass. Compare their names with the original files. If duplicates exist, delete the older version. To prevent this in future migrations, always run a delta pass before the final cutover scan.

If OneDrive Still Has Missing Files After the Delta Pass

Files are present on the source but SPMT does not see them

This usually means the source folder has a hidden system attribute or is a reparse point. Open an elevated Command Prompt on the source server. Run fsutil reparsepoint query "\\Server\Share\MissingFolder". If the output shows a reparse tag, the folder is a symbolic link or mount point. SPMT cannot migrate reparse points. You must copy the actual target folder content to a regular folder and then run the delta pass again.

The delta pass runs but uploads zero files

SPMT compares file timestamps to decide what to upload. If the file server clock is set to UTC and the OneDrive timestamp is in local time, SPMT may think the file is older. Check the time zone on the file server. Open Control Panel > Date and Time > Change time zone. Ensure it matches the time zone of the OneDrive tenant. Then run the delta pass again.

Files appear in OneDrive but cannot be opened

This happens when the file is corrupted or has an unsupported extension. SPMT uploads the file but OneDrive cannot render it. Go to the OneDrive library in a browser. Select the file and click Download. Try to open the downloaded file. If it fails, the source file is damaged. Restore the file from a backup and upload it manually to the same OneDrive folder.

Initial Full Scan vs Delta Pass vs Manual Upload: Key Differences

Item	Initial Full Scan	Delta Pass	Manual Upload
Purpose	Migrate all files from source to destination	Scan only new or modified files since last scan	Upload specific files that were missed
Time required	Hours to days depending on data volume	Minutes to a few hours	Seconds to minutes per file
Permission migration	Yes, if configured in SPMT settings	Yes, same as initial scan	No, permissions must be set manually or via PowerShell
Risk of duplicates	None if run once	Low if timestamps are accurate	High if file name already exists in destination
Best used for	First migration of a file share	Weekend cutover follow-up	Individual files that are locked or corrupted

After the delta pass and any manual uploads, run a final reconciliation by comparing the total file count on the source with the file count in the OneDrive library. Use the OneDrive admin center Reports > Usage to get the library file count. If the numbers match, the migration is complete.

To prevent missing files in future weekend cutovers, schedule the final delta scan to start 30 minutes after the official cutover window ends. Use the SPMT task scheduler to run the delta pass automatically. Also, enable the file server audit log to track files written during the cutover period so you can review them before declaring the migration finished.