Apple - Mysterious folders that appeared in Documents on upgrade to Big Sur

All of those folders could easily come from iCloud documents sync. You are correct to be cautious deleting them. I would be sure iCloud is signed out (or at least you don’t enable document sync) before trying to delete these.

We can’t really look at your iCloud settings, so a chat or call with Apple support would be prudent if you don’t see right away what happened to be sure you do not delete iCloud data.

Finder now shows documents belonging to some sandboxed applications.

No other application shows these extra folders. In particular Terminal commands and Finder replacements, like Path Finder and ForkLift, do not show the folders.

The folders are only present in Finder when an application has put data in the ~/Library/Containers/app/Data/Documents folder.

The applications I see in ~/Documents all have content in iCloud Drive though the files in iCloud Drive are not the same as in Finder.

In my case, I see the pseudo-folders for 3rd party applications like BBEdit, iThoughtsX.

This behaviour seems to be designed to mimic the behaviour of the Files application in iOS.

There is no known way to turn off this behaviour. But I would be glad to shown wrong on this.

It is not a good idea to just delete the folders or the files in them. Deleting the files is likely to cause problems when using the applications because the content has been created by the application.

My solution is to create a new folder ~/MyDocuments and put all my documents in there. That leaves ~/Documents for Apple to manipulate.

If you dislike this behaviour, submit feedback to Apple.