OneDrive for Business file server migration misses files for remote users: Fix Guide

Remote users report that after a file server migration to OneDrive for Business, specific files are missing from their synced folders. This problem occurs when the migration tool does not capture files that are open, locked, or stored in excluded paths during the transfer window. This guide explains the root causes of missing files in remote user sync folders after a migration and provides step-by-step fixes to locate and sync those files.

Why Files Are Missing for Remote Users After a File Server Migration

When you move files from a traditional file server to OneDrive for Business, the migration tool, such as the SharePoint Migration Tool or a third-party tool like Mover, copies files in batches. If a file is open in an application on the source server, locked by a system process, or located in a folder path that exceeds 400 characters, the tool skips that file and logs an error. Remote users who sync the target OneDrive library after the migration will not see these skipped files.

A second common cause is the migration tool’s default behavior of excluding system folders, hidden files, and temporary files. If the file server stored data in folders like AppData, Temp, or folders with ~ prefix names, those files are not copied. Remote users do not receive any notification about the exclusion.

A third cause involves network latency and bandwidth limits. Remote users who initiate a sync immediately after the migration completes may experience incomplete sync because the OneDrive sync client has not yet received the full file manifest from the server. The client shows a green checkmark but the file count is lower than expected.

Steps to Find and Sync Missing Files After Migration

Follow these steps in order to identify missing files and force them to sync to remote user devices.

1. Check the migration tool’s failed items report
   Open the SharePoint Migration Tool or your third-party migration tool dashboard. Locate the completed migration job. Download the CSV or text log file labeled FailedItems or Errors. This log lists every file that was not copied, the reason, and the source path. Sort by the ErrorCode column to group similar failures.
2. Resolve locked or open files on the source server
   For each file listed as FileInUse or SharingViolation, close the application on the file server that holds the file lock. Use the built-in Windows tool Computer Management > Shared Folders > Open Files to see who has the file open. After closing the lock, rerun the migration tool in incremental mode to copy only the previously failed files.
3. Copy excluded folder paths manually
   If the log shows PathTooLong or ExcludedFolder, open the source file server folder. Shorten the folder path by renaming deeply nested folders. Move files from excluded system folders such as AppData to a regular folder on the same drive. Then copy these files to the OneDrive target library using the OneDrive web interface or the sync client drag-and-drop.
4. Force a full resync on the remote user device
   On the remote user’s Windows device, right-click the OneDrive cloud icon in the system tray. Select Pause syncing and choose 2 hours. Wait 10 seconds. Right-click again and select Resume syncing. This forces the client to re-request the file list from the server. If missing files still do not appear, proceed to the next step.
5. Reset the OneDrive sync client
   Press Windows key + R, type %localappdata%\Microsoft\OneDrive\onedrive.exe /reset, and press Enter. Wait for the OneDrive setup window to appear. Sign in with the user’s work account. The client will re-scan the entire library. This step re-downloads the full file manifest and fixes sync state corruption.
6. Verify file count in the SharePoint admin center
   Go to Microsoft 365 admin center > SharePoint > Migration center. Select the migration job. Click Review migration jobs. Compare the Total files count with the Files synced count in the remote user’s OneDrive sync status. If numbers do not match, note the specific job ID and contact Microsoft Support with the job ID.

If OneDrive Still Shows Fewer Files Than Expected

Remote user sees a green checkmark but file count is wrong

This symptom usually means the sync client is healthy but the migration did not copy all files. Repeat step 1 to extract the full failed items log. Look for files with ErrorCode: 0x80070003 which indicates the source path no longer exists. Restore the source file from a backup or the file server’s previous version, then copy it to the OneDrive target manually.

Files appear in OneDrive web but not on the remote device

If the file exists in the OneDrive web interface at https://[tenant]-my.sharepoint.com but does not sync to the remote device, the sync client is likely filtering by file type or size. Open OneDrive settings > Sync and backup > Advanced settings > Files and Folders. Ensure Sync all files and folders is selected. Also check Files On-Demand is enabled so the client can download files on first access.

Migration tool log shows access denied for remote user’s files

When the migration tool runs under a service account that does not have read permissions to certain folders on the file server, those folders are skipped. Have the file server administrator grant the service account Read and List folder contents permissions on the root folder of the source share. Then rerun the migration tool in incremental mode.

Item	SharePoint Migration Tool (SPMT)	Mover (Microsoft 365 Migration Tool)
Best for	On-premises file servers and SharePoint Server 2010-2019	Cloud-to-cloud migrations (Box, Dropbox, Google Drive)
Reports failed items	CSV log with ErrorCode, SourcePath, and TargetPath	Summary report with per-file status via web dashboard
Handles locked files	Skips and logs; retries on incremental run	Skips and logs; no automatic retry
Path length limit	400 characters; truncates and logs as error	256 characters; fails silently
Supports incremental sync	Yes, after initial full scan	Yes, delta-based sync for 30 days

After completing the steps above, remote users can verify their file count by right-clicking the OneDrive cloud icon and selecting View sync problems. Any remaining missing files are listed there with a direct link to the file in OneDrive web. As a proactive measure, configure the migration tool to send a completion report via email to both the IT team and remote users so everyone knows when the migration is truly finished.