I have been trying to delete a couple of folders (via ftp) for one of my domains and I keep getting an error says "550 directory not empty". When this happens the folders will not delete. It doesnt happen on all domains just 1 of them.
This is usually due to hidden files (or directories) that begin with a dot (.). Look for a pref in your FTP program to Show Hidden (All) Files and turn that on, then start digging around to find that hidden file.