Record what changed
Note whether you turned off Desktop and Documents, disabled Drive entirely, signed out, or changed accounts. Those actions are different. Keep the approximate time and the choices you made in any macOS prompts.
Our first step is inspection rather than another settings change. Repeatedly toggling synchronization makes it harder to identify which folder contains the latest copy and can introduce more copies that need review.
Inspect local and cloud locations
Apple explains that turning off Desktop and Documents leaves the existing content in iCloud Drive while creating local folders. Open iCloud Drive in Finder and compare its Desktop and Documents folders with the folders in your home directory.
If you chose to keep a local copy when disabling Drive or signing out, check for the resulting iCloud Drive archive in your home folder. Verify its actual contents. A name or a remembered prompt is not proof that every file downloaded successfully.
Reconcile copies deliberately
Compare a few recognizable documents by content and latest edits. If the same name exists in both places, avoid overwriting either version until you understand which changes you need. Keep a separate copy before merging important work.
Our recommended trial is one completed document copied to the intended nonsynced destination. Confirm it opens from that path. For a large collection, make a list of expected folders and verify the result before considering cleanup.
If an item is still missing
Check the intended Apple Account on iCloud.com and use Recently Deleted if actual deletion may have occurred. If a different device still has a needed version, preserve it before making further edits or changes to sync settings.
iCloud Doctor inspects accessible Drive items, not every prior account state or deleted file. An empty or unavailable scan cannot prove your cloud data is gone. Use the recovery guide or Apple support when you cannot locate the original.
References & further reading
These guides combine the linked official guidance with ClearDisk’s documented behavior. Your files and app settings determine the right next step.