OneDrive for Business file server migration misses files for phased migrations: Fix Guide

When you run a phased migration from a file server to OneDrive for Business, some files do not appear in the destination folders. This problem typically occurs because the migration tool does not re-scan the source for new or changed files after the initial pass. In a phased migration, you move batches of users or folders over days or weeks, but files added or modified in the source after the first scan are skipped. This article explains why the tool misses files in phased scenarios and provides the exact steps to locate and transfer the missing items.

Why Phased Migrations Miss Files in OneDrive for Business

Phased migrations use the Microsoft 365 Migration Manager, which scans the source file server once when the task is created. The tool copies the scanned files to the target OneDrive folder, but it does not continuously monitor the source for new or changed files. If a user or admin adds a file to the source folder after the initial scan, that file is not included in the migration batch. This behavior is by design to avoid re-scanning terabytes of data on every run.

The problem becomes more visible when migrations span several days. For example, a department might continue working on shared files while the IT team migrates their folders. The files created or modified after the scan date remain on the file server and never reach OneDrive. The migration report shows these files as “not found” or “skipped,” but the report often does not list them explicitly.

Another contributing factor is the retention of source folder permissions. When the Migration Manager copies a file, it preserves the NTFS permissions. If the source folder has inheritance disabled or contains explicit DENY entries, the tool may skip the file entirely without logging an error. This behavior is not specific to phased migrations, but the delay between scans increases the chance that permission changes occur during the migration window.

How the Migration Manager Scans Source Folders

The Migration Manager creates a scan task that enumerates all files and folders in the specified source path. The scan records file size, last-modified date, and permissions. Once the scan completes, the tool starts the copy phase. It compares the scanned list against the destination and copies only items that do not already exist in the target. Because the scan is a snapshot, any file added after the snapshot is invisible to the tool.

File Exclusions in the Default Configuration

By default, the Migration Manager excludes files that match certain patterns: temporary files ending in .tmp, files larger than 250 GB, files with names longer than 400 characters, and files with characters not supported by OneDrive. If a file falls into one of these categories, it is skipped silently. The migration report lists these as “skipped due to exclusion rules,” but the log is easy to overlook in large migrations.

Steps to Recover Missing Files in a Phased Migration

The following steps assume you are using the Microsoft 365 Migration Manager for file server migrations. If you are using a third-party tool, the same logic applies: you must force a re-scan of the source folder after the initial migration completes.

1. Open the Migration Manager in the Microsoft 365 admin center
   Go to Admin centers > Migration Manager. Select the migration task that corresponds to the phased migration where files are missing.
2. Review the migration report for skipped files
   Click View details on the task. Look for the row labeled “Skipped items.” Expand that row to see the file names and the reason for skipping. Common reasons include “File modified after scan” or “File excluded by filter.”
3. Run a re-scan of the source folder
   In the task details pane, click Actions > Re-scan. The tool will re-enumerate the source folder and detect any files that were added or changed since the last scan. This step does not re-copy files that already exist in the destination.
4. Adjust the source filter to include recent modifications
   Before running the re-scan, set the filter to include files modified within the last 7 days. Go to Task settings > Source filters and change Last modified to Within the last 7 days. This reduces the scan scope and speeds up the process.
5. Manually copy any files that the re-scan still misses
   If the re-scan does not capture all missing files, use a file copy tool such as Robocopy with the /MIR switch to mirror the source folder to a temporary location, then upload those files to OneDrive using the OneDrive sync app. Example command: robocopy \fileserver\share \temp\migration /MIR /COPY:DAT /R:3 /W:5
6. Verify the destination OneDrive folder has enough space
   Check the OneDrive storage quota for the target user. If the user has exceeded their quota, new files will not sync. Go to Microsoft 365 admin center > Users > Active users > OneDrive settings and increase the storage limit if needed.

If OneDrive Still Has Missing Files After the Re-Scan

Files excluded due to name or path length

OneDrive for Business does not support file names longer than 256 characters or paths longer than 400 characters. The Migration Manager skips these files without error. To fix this, shorten the file name or folder path on the source server, then run the re-scan. Use a PowerShell script to identify files with long paths: Get-ChildItem -Path \fileserver\share -Recurse | Where-Object { $_.FullName.Length -gt 400 }

Files with unsupported characters

OneDrive does not allow the following characters in file names: " : < > ? / \ |. The Migration Manager skips files containing these characters. Rename the files on the source server, replacing the unsupported characters with a hyphen or underscore. Then run the re-scan.

Permission errors causing silent failures

If the migration account does not have read access to a file or folder, the tool skips it. Check the NTFS permissions on the source folder. The migration account must have at least Read & Execute and List folder contents permissions. Use the Effective Access tab in the folder properties to verify.

Phased Migration vs One-Time Full Migration: Key Differences

Item	Phased Migration	One-Time Full Migration
Scan frequency	Single scan at task creation; manual re-scan required for new files	Single scan, copied in one batch
Best for	Large data sets where users cannot stop working	Small to medium data sets where source can be frozen
Risk of missing files	High, because files added after the scan are skipped	Low, because the source is frozen before the scan
User experience	Users can keep working; IT handles gaps later	Users must pause work during migration

Phased migrations require ongoing monitoring and periodic re-scans. A one-time full migration is simpler but forces a cutover date where all users stop modifying files on the source server.

After you complete the re-scan and copy the missing files, verify that all items appear in the target OneDrive folder. Open OneDrive in File Explorer, right-click the folder, and select Check for updates. If any files still show a red X, confirm that the user has the OneDrive sync app running and that the sync status is healthy.

For future phased migrations, schedule a re-scan every 24 hours during the migration window. This catches files that are added overnight. You can automate the re-scan using the Start-MigrationTask PowerShell cmdlet with the -ReScan parameter. This reduces the chance of missed files and eliminates manual checks.