Deleted Desktop & Documents Folders from iCloud Drive, but still takes up space
I had to leave this as an answer, because it's too long to explain in the comments section.  I'm not guaranteeing that your invisible 13GB of files are definitely hanging around in the iCloud trash, but it's just the most obvious first guess that I could think of.  So, let's find out:

Open up Terminal and type in this command:

cd ~/Library/Mobile\ Documents/com~apple~CloudDocs


That will take you to the local storage folder where iCloud keeps copies of your files on your computer.  Type ls to list the files in the directory if you're curious, but it's much the same as navigating to your iCloud folder in Finder.

However, what you actually want to do is see if the iCloud trash is still full of files that are taking up space:

du -d1 .Trash


Hopefully, it'll contain about 13GB of files in it.  If this is the case, and you're sure there's nothing in the trash folder you wish to keep, just delete the folder:

rm -R .Trash


This is permanent and cannot be undone.  So be sure you're happy to lose those files in the trash.

Then type exit and quit Terminal.