OneDrive Admin Checklist: file server migration misses files for phased migrations

When you run a phased migration from an on-premises file server to OneDrive, some files do not appear in the destination. This problem typically occurs because the migration tool skips files that were modified after the initial scan or because folder permissions prevent the tool from reading certain items. The result is an incomplete migration that leaves users without access to important documents. This article explains why files are missed during phased migrations and provides a checklist to verify and fix the gaps.

Why Phased Migrations Miss Files

Phased migrations move data in batches over several days or weeks. The Microsoft 365 Migration Manager scans the source file server at the start of each batch. Files created or modified after that scan are not included in the batch unless the admin triggers a new scan. Common technical causes include:

• Stale scan cache: The migration tool caches the file list from the initial scan. If you do not refresh the scan before the next batch, new files remain unknown to the tool.
• Permission mismatches: The account that runs the migration must have Read access to every folder and file. A single folder with broken inheritance can cause all files inside it to be skipped.
• File locks and open handles: Files that are open in an application when the migration agent tries to copy them are skipped. The tool does not retry these files automatically.
• Path length limits: Windows has a 260-character path limit for the source file server. Files with longer paths are not migrated unless the admin enables long path support.

The migration tool records each skipped file in the task log but does not alert the admin. You must review the logs manually after each batch to catch missing items.

Checklist to Find and Fix Missed Files in Phased Migrations

Use the following steps after each batch to verify that all files were moved. Run these checks before starting the next batch.

Step 1: Refresh the source scan before each batch

1. Open Migration Manager
   Go to the Microsoft 365 admin center at admin.microsoft.com. Select Migration Manager under the Admin centers section.
2. Select the source connection
   Click Sources and choose your file server connection. Click Scan to refresh the file inventory. Wait for the scan to complete before creating the next batch.
3. Compare file counts
   Compare the total file count from the new scan with the count from the previous scan. A significant increase indicates that files were missed earlier.

Step 2: Review the task failure log for each batch

1. Open the batch details
   In Migration Manager, click Tasks. Find the batch you want to review and click the batch name.
2. Filter for failed items
   Click Filter and select Failed. The list shows every file that the tool could not copy.
3. Read the failure reason
   Hover over the failure icon next to each file. Common reasons include “Access denied,” “File in use,” and “Path too long.”
4. Export the failure list
   Click Export to download a CSV of all failed files. Use this list to fix permissions or retry files in the next batch.

Step 3: Verify permissions on the source folder structure

1. Check the migration account
   Confirm that the account used for the migration has at least Read and List Folder Contents permissions on the root folder of the file server share.
2. Test a random subfolder
   Log in to the file server with the migration account. Navigate to three random subfolders that had files in the failure log. Try to open a file in each folder.
3. Fix broken inheritance
   If you cannot open a file, right-click the folder, select Properties, go to the Security tab, and click Advanced. Enable inheritance if it is disabled.

Step 4: Retry failed files in the next batch

1. Create a new batch
   In Migration Manager, click Create batch. Select the same source and destination as the previous batch.
2. Import the failure CSV
   Choose Import from CSV and upload the CSV you exported in Step 2. The tool will attempt to migrate only those files.
3. Run the batch and review
   After the batch completes, check the task log again. Any files that still fail need manual handling.

If Files Are Still Missing After the Checklist

Some file types and configurations require additional steps. Use the subsections below to address persistent issues.

Files with long paths (over 260 characters)

Windows 10 and Windows 11 support long file paths only when the Group Policy setting Enable Win32 long paths is enabled on the file server. To fix this:

1. Open Local Group Policy Editor on the file server.
2. Go to Computer Configuration > Administrative Templates > System > Filesystem.
3. Enable Enable Win32 long paths.
4. Restart the file server and run a fresh scan in Migration Manager.

Files open in applications during migration

The migration agent cannot copy a file that is locked by another process. To minimize skipped files:

• Schedule migrations during off-peak hours when fewer users are working on files.
• Notify users to close files before each batch starts.
• Use the Volume Shadow Copy service on the file server. Migration Manager can read shadow copies to access locked files.

Hidden files and system files

Migration Manager skips files with the Hidden or System attribute by default. To include these files:

1. In Migration Manager, go to Settings.
2. Under Migration options, enable Include hidden and system files.
3. Run a new scan and create a batch that targets the missed folders.

Migration Manager Scan vs Task Log: What Each Reports

Item	Scan Report	Task Log
Purpose	Lists all files and folders on the source before migration starts	Shows the result of the copy operation for each file
When to review	Before creating a batch to confirm the file inventory is current	After a batch completes to find files that failed to copy
What it includes	File name, path, size, last modified date, and permissions	File name, path, status Succeeded or Failed, and error code
Can it be exported	Yes, as a CSV from the source details page	Yes, as a CSV from the task details page

Phased migrations require you to refresh the source scan before each batch and review the task log after each batch. Run the checklist steps in order after every batch to catch missed files. For files that still fail after retrying, check the file server for long paths, open handles, and hidden attributes. The failure log in Migration Manager gives you the exact file path and error code for each skipped item, so you can fix the root cause and migrate the file in the next batch.