But before you do what Bob suggested, make sure you copy the documents to some other folder than Documents. What I think works is to keep logged into iCloud and create a set of three folders outside of Documents, Desktop or Downloads. Now copy whatever is in Documents to one of the three folders. That process may take a while, depending on your internet speed and number of files to be copied. Repeat for the other two folders. Once you have all three competed, you can then follow Bob's directions in #3 and disconnect from iCloud. At that point your Documents, Desktop and Downloads will show as empty because it's lost the connection (I think, I don't use it myself). Move the contents of the three new folders to the appropriate folder and then delete the three new folders.
I didn't suggest using TM because I don't know if TM actually backs up the real files from iCloud or not. I think it does not, but again, I don't use iCloud for Docs, Desktop or Downloads, so I have no real experience with it. But logic says that given the real files are NOT on your machine, TM won't back them up.
Maybe somebody who actually uses iCloud for documents will come along a correct my directions, but that is what I read somewhere.