Hi there @Edgewood, thanks for checking in with us.
You're right, since the files are in your Dropbox folder, if you delete them, they'll be removed from your account, and any other connected device.
What automatically uploaded your Documents, Downloads, and Desktop folders is computer backup.
For this reason, you'll have to turn it off before moving the files back to their original locations.
Let me know how it goes, cheers!