Disable Documents and Desktop iCloud sync but keep all files locally?
Solution 1:
You could hold down the option + click on the document folder and drag it to another directory (essentially copying it) and then disable sync, so it does not affect the files you just created. Do the same for the Desktop Folder.
Best if you can copy to an external drive, to avoid any chances of losing the local files, until you resolve the unsync and deletion of said files.