Urgent Assistance Required: Resolving SharePoint Online Syncing and Folder Duplication Issues

Hi Vance Ethan,
Thank you for posting question to Microsoft Q&A Forum.I’d check the missing files and misplaced folders separately first. There isn’t enough information yet to say they have the same cause. Also, the name shown under “Modified By” alone does not tell us who moved or copied a folder.

1/ Check the missing files on one affected computer.

Open the same folder in SharePoint and File Explorer using the same work account.

If the files appear with blue cloud icons, they are available online but haven’t been downloaded. For folders needed offline, right-click the folder > Always keep on this device, then wait for the download to finish. Make sure the computer has enough free space. This setting helps with offline access; it does not fix files that are completely missing from Explorer. See Microsoft’s Files On-Demand guide.

If the files don’t appear at all, click the OneDrive cloud icon near the Windows clock and check for errors or a “Processing changes” message. Then go to OneDrive Settings > Account > Choose folders and check that the folders you need are selected.

Also check whether anyone previously used the Sync button for that library. Microsoft explains that you cannot use Sync and Add shortcut to OneDrive together for the same library. This is worth checking, but it does not prove what caused the misplaced folders. See Microsoft’s troubleshooting article.

Your IT admin should also check the number of items being synced and the names and paths of affected files against Microsoft’s sync restrictions.

2/ Check what happened to one misplaced folder.

Does it also appear in the wrong location when you open SharePoint in a browser? Is the original folder still there, and is the new item a folder or just a shortcut?

If the change appears in SharePoint online, ask your IT admin to check Microsoft Purview Audit around the time it happened. They can look for folder creation, copy, move, and rename events, then review the account and folder details recorded. Microsoft lists these in its folder audit activities guide.

Your admin should also check the person’s access to both the original and new locations, including access through groups or shared links. Their access today may differ from what they had when the change happened. These checks will help avoid blaming someone based only on “Modified By.”

Could you share:

• When this started, and whether it affects everyone or only certain staff or libraries.
• Whether the missing files are absent from Explorer or appear but won’t open.
• The OneDrive version, any sync error, and the approximate number of items being synced on one affected PC.
• Whether the misplaced folders also appear in SharePoint online and whether the originals remain.

Please hide names, email addresses, and other sensitive information in any screenshots.

If folders keep appearing in the wrong places, your admin should also contact Microsoft 365 support, with one example, the time it happened, and any available audit records. The right fix will depend on what those checks show.

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