Certain files lost when removing iCloud sync

I recently removed the documents and desktop sync with iCloud. I know the files were stored locally in the library/mobile documents, but when I moved the files back to their normal places, I am missing a few folders. I dragged and dropped the whole documents folder in the the local documents and the desktop folder contents onto the desktop. Most things are back in place, but I am missing a few.

I see the files when searching for them in the finder, but I cannot open them, and there is no given file path. I can find the file path for other files, but not the missing ones.

Any suggestions?