During a merger or acquisition, IT teams often migrate file server data to OneDrive for Business. A common failure pattern is that some files do not appear in the target OneDrive libraries after the migration tool reports success. This problem typically occurs because of file naming conflicts, path length limits, or permission inheritance issues that the migration tool does not resolve automatically. This article explains why files are missed during a merge migration and provides a step-by-step fix to locate and transfer those missing items.
Key Takeaways: Fixing Missing Files in OneDrive After a Merger Migration
- SharePoint Migration Tool > Reports > Failure Report: Use this report to identify every file that failed to transfer and the exact error reason.
- Windows File Explorer > File Path Length Check: Files with paths longer than 400 characters are silently skipped by default; shorten or move them before retrying.
- OneDrive Sync Client > Pause Syncing: Pause the sync client during the migration to prevent file locks and version conflicts that cause omissions.
Why OneDrive File Server Migrations Miss Files During Mergers
When you use the SharePoint Migration Tool or a third-party tool to move file server data to OneDrive for Business, the tool scans the source folder structure and uploads each file to the target library. During a merger, the source environment often contains data from multiple legacy domains, file servers, and naming conventions. The migration tool applies a set of rules to determine which files can be moved and which must be skipped.
The root cause of missing files is almost always one of the following three conditions:
File Name and Path Length Restrictions
OneDrive for Business and SharePoint Online enforce a maximum file path length of 400 characters. If a file on the source server has a path longer than 400 characters, the migration tool skips it without an obvious warning. Merger data often includes deeply nested folder structures from multiple companies, which easily exceed this limit.
File Name Character Conflicts
Windows file servers allow certain characters that OneDrive does not accept. The characters " : < > ? / \ | are illegal in SharePoint and OneDrive. Files containing these characters in their names are skipped by the migration tool. Merger data frequently includes files with special characters from legacy systems.
Permission and Lock Conflicts
If a file is open or locked by another user or process during the migration scan, the tool cannot read the file and omits it. During a merger, multiple IT teams may be accessing the same file server simultaneously, increasing the chance of file locks.
Steps to Locate and Migrate Missing Files
Follow these steps in order to identify every file that was missed and successfully migrate it to OneDrive for Business.
- Generate the migration failure report
Open the SharePoint Migration Tool. Click on the migration job name that was used for the merger. Select View Reports and then Failure Report. Download the CSV file. This file lists every file that failed to migrate and the specific error code for each failure. - Identify files with long paths
Open the failure report CSV in Excel. Sort by the ErrorCode column. Look for error code SPO_FailedPathLengthLimit. These files have paths exceeding 400 characters. Copy the full source path for each file. - Shorten file paths on the source server
On the source file server, move the files with long paths to a shorter folder structure. For example, move\\ServerA\Data\Dept\Project\Sub\File.docxto\\ServerA\Data\File.docx. Do not rename the file itself unless the name contains illegal characters. - Fix illegal characters in file names
In the failure report, look for error code SPO_FailedIllegalCharacter. Open the source folder in Windows File Explorer. Rename each file to remove the illegal characters. Replace" : < > ? / \ |with an underscore or hyphen. - Pause OneDrive sync on all target machines
On each user computer that syncs the target OneDrive library, right-click the OneDrive icon in the system tray and select Pause syncing. Choose 2 hours. This prevents file locks during the migration retry. - Create a new migration job for the corrected files
In the SharePoint Migration Tool, click New Migration. Select File Share as the source. Browse to the folder that now contains the corrected files. Set the destination to the same OneDrive library that was used in the original job. - Run the migration job and verify
Start the new migration job. After it completes, open the failure report again. Confirm that the error count is zero. Open the target OneDrive library in a web browser and verify that the files appear.
If OneDrive Still Has Missing Files After the Main Fix
If the failure report shows no errors but files are still missing from the target OneDrive library, check the following scenarios.
Files Were Migrated But Overwritten by Sync Conflicts
When two files with the same name are migrated from different source folders, only the last one written survives. The migration tool does not merge file content. To recover the overwritten file, open the OneDrive library in a web browser, click the file name, and select Version History. Look for the earlier version that was migrated first. Restore it if needed.
Files Existed in Multiple Source Locations But Only One Copy Transferred
If the same file was present in two different source folders and both were mapped to the same target library, the migration tool deduplicates by file name. The second copy is skipped. To preserve both copies, rename one version on the source before retrying the migration.
Files Were Excluded by Tenant Policy
Your Microsoft 365 tenant may have file type blocking policies for OneDrive. Common blocked types include .exe, .ps1, .vbs, and .zip. Open the Microsoft 365 admin center, go to Settings > Org settings > OneDrive, and check the Block file types list. If a missing file type is listed, remove it from the block list or change the file extension before migration.
| Item | SharePoint Migration Tool | Manual Drag-and-Drop |
|---|---|---|
| Error reporting | Produces a detailed failure CSV with error codes | No error report; files are silently skipped |
| Path length handling | Skips files over 400 characters; no auto-fix | Skips files over 400 characters; no auto-fix |
| Batch processing | Supports thousands of files in one job | Manual per-file upload; impractical for mergers |
| Permission migration | Copies NTFS permissions to SharePoint if enabled | Resets permissions to default library settings |
After completing the steps above, you can now identify and migrate every file that was missed during the original OneDrive file server migration for the merger. Run the failure report again after the retry to confirm zero errors. As an advanced tip, enable the Preserve file version history option in the SharePoint Migration Tool settings before the retry to capture previous versions of overwritten files.