How to delete ghost OneDrive files?

Hi @bill

Since OneDrive itself says “Item does not exist. It may have been deleted by another user”, avoid reconnecting your PC and trying another sync/delete cycle for now. First, determine whether these are actual DriveItem objects still present in OneDrive or only stale references being displayed by OneDrive/OneNote.

For the OneNote notebooks specifically, Microsoft normally expects you to delete the notebook from OneDrive itself, and then close the deleted notebook in OneNote. Otherwise, a deleted notebook can keep appearing in OneNote's notebook list even though the underlying notebook no longer exists.

Since you've already looked at Microsoft Graph, use it to confirm whether the problematic item actually exists, rather than relying on what the OneDrive web UI displays. For example, enumerate/search the drive and obtain the actual DriveItem ID for one problematic item. Microsoft Graph exposes OneDrive files and folders as driveItem resources and supports searching the drive hierarchy.

If Graph returns a real DriveItem ID, that gives you something concrete to work with. Graph supports deleting a DriveItem, and it now also has a permanentDelete operation that permanently removes an item by ID rather than sending it to the recycle bin. Use permanent deletion only after confirming the ID is definitely the unwanted item, since it cannot be restored afterward.

On the other hand, if the OneDrive web interface displays the item but Graph cannot retrieve it by ID/path and opening it consistently returns “Item does not exist,” do not keep trying local deletion tricks. That points more to a stale/orphaned service-side reference or view than a normal file the sync client can remove.

Since your goal is to purge OneDrive completely, Microsoft also has a documented procedure specifically for that: unlink the PC first, delete the cloud contents through OneDrive.com, remove shared-folder shortcuts separately, and finally empty the OneDrive recycle bin.

Before doing that, check three places in OneDrive.com: My Files, Shared, and Recycle Bin. Shared-folder shortcuts matter because Microsoft treats them differently from files you own. You remove the shortcut rather than deleting the underlying shared content.

If those ghost entries remain after the underlying DriveItems are gone and the recycle bin has been cleared, treat this as a OneDrive service-side metadata issue and contact OneDrive support rather than reconnecting the sync client.

If you can post the Graph response for one affected item, particularly its id, name, parentReference, webUrl, and whether it has file, folder, remoteItem, or package properties, with personal information removed, we can determine the appropriate next step.

References:

Delete files or folders in OneDrive

Delete a OneNote notebook

Permanently delete your entire OneDrive

Microsoft Graph driveItem resource

Microsoft Graph permanentDelete

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