I would create two new folders in your user home folder "DocumentsLocal" and "DesktopLocal".
- Drag the files and folder you are seeing in you iCloud Documents folder to "DocumenstLocal", to. remove them from iCloud.
- Drag the files and folder you are seeing on your iCloud Desktop to "DesktopLocal".
Before you drag an item, click the download arrow in the cloud symbol to the right of the filename to download it, if you are seeing a cloud symbol.
Wait for all files to copy back to these local folders. Only then disable Desktop & Documents in the System Preferences iCloud and move the items from your temporary folders back to your regular Desktop and Documents folders
If really are files missing, it will be better to restore your Desktop and Documents folders from the last Time Machine backup you made before you enabled iCloud Desktop & Documents.