OneDrive for Business Known Folder Move troubleshooting for domain profile migrations: creates duplicate folders

When migrating user profiles from one domain to another, IT administrators often enable OneDrive for Business Known Folder Move to redirect Desktop, Documents, and Pictures to the cloud. After the migration, users may see duplicate folders appear in their OneDrive—one set named with the old domain profile and another set with the new domain profile. This happens because Known Folder Move links the redirected folders to the user’s Windows profile SID, and a domain migration changes that SID without updating the OneDrive sync relationship. This article explains why duplicate folders occur, provides step-by-step instructions to resolve the issue, and covers related failures you may encounter during domain profile migrations.

Why Known Folder Move Creates Duplicate Folders After a Domain Migration

Known Folder Move redirects the Windows user folders Desktop, Documents, and Pictures to OneDrive by creating a symbolic link in the user profile that points to the OneDrive sync location. This link is tied to the user’s security identifier, or SID, which is generated by the local domain controller when the user account is created. When you migrate a user profile from an old domain to a new domain, the user receives a new SID. OneDrive does not automatically update the existing Known Folder Move configuration to match the new SID. Instead, the sync client sees the old redirected folders as orphaned and creates a new set of folders under the new SID’s profile. The result is two sets of folders in OneDrive—one from the old domain profile and one from the new domain profile.

The duplicate folders are not a sync error in the traditional sense. They are a consequence of the sync client treating the new profile as a separate device or user identity. The old folders remain in OneDrive because they are still associated with the original sync relationship. If you simply re-enable Known Folder Move on the new profile without unlinking the old one, the client creates a second copy of the folders rather than reusing the existing cloud folders.

How the Old SID Persists in OneDrive Configuration

When Known Folder Move is first enabled, OneDrive writes the user’s SID and tenant ID into the Windows registry under HKEY_CURRENT_USER\Software\Microsoft\OneDrive\Accounts\Business1. This registry key also stores the folder redirection paths. After a domain migration, the old SID remains in this key even though the user now logs in with a new SID. OneDrive reads the old SID during sync initialization and compares it to the current profile SID. Because they do not match, the client assumes the Known Folder Move configuration is invalid and creates a new configuration using the new SID. The old registry entries are not deleted automatically, which is why the duplicate folders appear.

Steps to Remove Duplicate Folders and Reconfigure Known Folder Move

Follow these steps in order on each affected user’s machine. You must perform these steps after the domain migration is complete and the user is signed in with the new domain account.

1. Back up the existing OneDrive folders
   Before making any changes, ensure the duplicate folders in OneDrive are backed up. Open File Explorer, navigate to the OneDrive folder, and verify that the old domain folders contain the expected files. If they do, copy them to a local folder outside OneDrive to avoid accidental data loss.
2. Unlink OneDrive from the old profile
   Right-click the OneDrive cloud icon in the system tray. Select Settings. Go to the Account tab. Click Unlink this PC. Confirm the prompt. This removes the current sync relationship but does not delete local files.
3. Clear the old registry entries
   Press Windows key + R, type regedit, and press Enter. Navigate to HKEY_CURRENT_USER\Software\Microsoft\OneDrive\Accounts\Business1. Delete the entire Business1 key. If multiple Business keys exist, delete all of them. Close Registry Editor.
4. Restart the OneDrive sync client
   Press Ctrl + Shift + Esc to open Task Manager. Find Microsoft OneDrive in the Processes list, right-click it, and select End task. Open the Start menu, type OneDrive, and press Enter to restart the client.
5. Sign in with the new domain account
   In the OneDrive setup window, enter the new domain user’s email address and password. Complete the initial setup. Do not enable Known Folder Move during this step.
6. Move the old cloud folders into the new OneDrive root
   Open OneDrive in File Explorer. Locate the duplicate folders from the old domain. Move all files from the old folders into the corresponding new folders that OneDrive created. For example, move files from OldDomain\Documents to NewDomain\Documents. After moving, delete the empty old folders from OneDrive.
7. Enable Known Folder Move on the new profile
   Right-click the OneDrive system tray icon and select Settings. Go to the Sync and backup tab. Click Manage backup. Select the folders you want to redirect—Desktop, Documents, and Pictures. Click Start backup. OneDrive will redirect the new profile folders to the cloud location you just populated.
8. Verify the folder redirection
   Open File Explorer and check that the Desktop, Documents, and Pictures folders in the user profile now point to OneDrive. Right-click one of these folders, select Properties, and confirm the Location tab shows a OneDrive path.

If OneDrive Still Has Issues After the Main Fix

OneDrive Keeps Prompting to Back Up Folders That Are Already Redirected

After re-enabling Known Folder Move, the sync client may continue to show a notification asking you to back up important folders. This occurs when the registry still contains remnants of the old folder redirection. Open Registry Editor and navigate to HKEY_CURRENT_USER\Software\Microsoft\OneDrive\Accounts\Business1. Look for a key named KfmFolderHistory or KfmEnabled. Delete these keys if they exist. Restart OneDrive again to clear the notification.

Duplicate Folders Reappear After a Few Days

If duplicate folders return after the fix, the user’s profile may have been migrated again or the old SID was not fully removed. Run the command whoami /user in a Command Prompt to confirm the current SID matches the one in the OneDrive registry key. If the SID still differs, repeat the unlinking and registry cleanup steps. Additionally, check Group Policy to ensure no policy is forcing Known Folder Move to use the old profile path.

Files Are Missing After Moving Them Out of the Old Folders

When you move files from the old duplicate folders into the new folders, the files are removed from the old cloud location. If the old folders were shared with other users, those users lose access to the files. Before moving files, notify affected users and create a share link for the new folder location. Use the OneDrive web interface to verify that file permissions are preserved after the move.

Known Folder Move vs Manual Folder Redirection: Key Differences

Item	Known Folder Move	Manual Folder Redirection
Setup method	OneDrive Settings > Sync and backup > Manage backup	Folder Properties > Location tab > Move
Automatic sync	Redirects folders to OneDrive with continuous sync	Requires manual copy and OneDrive folder selection
Duplicate protection	Creates symbolic links to prevent duplication	No duplicate protection; manual copies may create duplicates
Domain migration handling	Does not update SID automatically; may cause duplicates	No SID dependency; folders remain in place but must be re-linked
Group Policy support	Supports enforced move via OneDrive administrative templates	Supports Group Policy Folder Redirection but not OneDrive sync

You can now resolve duplicate folders caused by Known Folder Move during domain profile migrations. After unlinking the old sync relationship and clearing the registry entries, reconfigure Known Folder Move on the new profile to restore seamless folder redirection. As an advanced tip, use the OneDrive admin center to monitor Known Folder Move adoption reports and verify that all migrated users have the correct folder configuration. This prevents duplicate folders from appearing in future domain migrations.