OneDrive Migration Tool Reports Success but Files Are Missing

You completed a OneDrive migration using the SharePoint Migration Tool or a third-party tool. The tool showed a green checkmark and reported zero errors. Yet when you open the destination OneDrive account, files you expected to see are not there. This mismatch between tool output and actual file presence is a known problem. It usually happens because the migration tool counts the transfer of metadata or folder structure as success, even when file content fails to upload or gets blocked by sync rules. This article explains why the tool reports success with missing files and gives you exact steps to find and recover those missing items.

Why the Migration Tool Reports Success When Files Are Missing

Migration tools for OneDrive evaluate success at the job level, not the file level. A job that completes with 100 percent of folders created and metadata copied is marked as successful. Individual file uploads can fail silently within that same job. Common causes include file names that exceed the 400-character path limit, files with invalid characters such as a tilde or colon, and files larger than the OneDrive upload limit of 250 GB per file. The tool counts the folder as migrated and reports success, but the actual file content never reached the destination.

Another cause is the OneDrive sync app interfering with the migration. If the destination OneDrive is syncing to a local folder while the migration runs, the sync app can lock files or reject changes that conflict with its own upload queue. The migration tool sees the destination path as writable and reports success, but the sync app later discards or quarantines the incoming file. The user sees zero files in the cloud, even though the migration tool shows green.

Permission inheritance can also create this problem. When files are migrated into a library that has unique permissions, the migration tool may copy the file but fail to set the correct sharing settings. The file exists in the cloud but is invisible to the end user because their account lacks read access. The tool reports success because the upload operation itself completed.

Steps to Locate and Recover Missing Files After Migration

Follow these steps in order. Do not rerun the migration until you identify why files are missing.

1. Open the SharePoint Migration Tool detailed report
   Launch the SharePoint Migration Tool. Click the completed job. Select View report. Look for the Detailed report button. Download the CSV file. Open the CSV in Excel. Filter the Status column for values other than Passed. Look for Warning or Failed entries. Each row shows the exact file path and error code. Common error codes include 0x80070057 for invalid file names and 0x80070490 for file size limits.
2. Check the OneDrive admin center migration reports
   Go to the Microsoft 365 admin center. Select Reports then Usage. Click OneDrive. Choose Migration status. This report shows all migration jobs across your tenant. Click a job to see files that were skipped, blocked, or partially transferred. Export this report as a CSV for further analysis.
3. Search the destination OneDrive directly
   Open a browser and go to https://www.office.com. Sign in as the affected user. Open OneDrive. In the search box at the top, type a unique word from a known missing file name. If the file appears in search results but not in the folder view, the file exists but is hidden because of permission inheritance. Check the folder permissions in the OneDrive web interface by clicking the folder, selecting Manage access, and confirming the user has at least Read access.
4. Check the OneDrive recycle bin
   In the destination OneDrive web interface, click Recycle bin in the left navigation. Files that were uploaded but then deleted by the sync app or a policy rule appear here. If you see the missing files, select them and click Restore. Also check the Second-stage recycle bin at the bottom of the recycle bin page. Files remain there for up to 93 days.
5. Pause OneDrive sync and rerun the migration for the affected folder
   Right-click the OneDrive cloud icon in the system tray. Select Pause syncing and choose 2 hours. In the SharePoint Migration Tool, create a new job that targets only the folder containing the missing files. Set the migration mode to File only to skip folder creation. After the job completes, resume OneDrive sync by right-clicking the cloud icon and selecting Resume syncing.

If OneDrive Still Shows Missing Files After the Main Fix

Files with invalid characters were renamed or skipped

OneDrive does not accept file names with a tilde, a leading space, a trailing period, or a colon. The migration tool may rename these files by replacing the invalid character with an underscore. Search the destination for the renamed version. To avoid this in future migrations, use the File name handling setting in the SharePoint Migration Tool and choose Replace invalid characters with underscores.

File version history was lost

The migration tool copies only the latest version of each file by default. If the source contained multiple versions, only the most recent one appears in the destination. This is not a missing file — it is a missing version. To migrate version history, enable the Preserve file version history option in the SharePoint Migration Tool job settings before running the migration.

Files were blocked by OneDrive sync restrictions

Tenant-level settings in the OneDrive admin center can block specific file types. Go to the Microsoft 365 admin center. Select Settings then Org settings. Click OneDrive. Under Sync, check Block syncing of specific file types. If your missing files match the blocked list, remove the file type from the block list and rerun the migration for those files only.

Migration Tool Report vs Actual File Presence: Key Differences

Item	Migration Tool Report	Actual File Presence in OneDrive
Success criteria	Job completion and folder creation	Every file byte uploaded and accessible
Error visibility	Summary shows green checkmark	Detailed CSV shows per-file warnings
Permission handling	Copies files regardless of user access	File invisible if user lacks read permission
File name validation	Skips or renames invalid names silently	Rejects names with tilde, colon, or leading space
Sync interference	Not detected by the migration tool	Sync app can delete or quarantine uploaded files

You can now locate files that the migration tool reported as successfully transferred but that are missing from the destination OneDrive. Start by downloading and filtering the detailed migration CSV report. Then check the OneDrive recycle bin and the user’s folder permissions. If you find files that were renamed due to invalid characters, use the file name handling setting in the SharePoint Migration Tool before rerunning the job. As an advanced step, enable the Preserve file version history option to ensure all versions transfer correctly in your next migration.