The safest way to delete files is via FTP. It's not as easy as to delete files/torrents via the gui (rtorrent etc), but everything is deleted via FTP. I have noticed that when i delete via the guy some files remain on the server and take HDD space, while you can't see those files on the client (rtorrent etc).
he have to do it both ways, deleting trough FTP will delete the files but the torrent will still remain in the GUI and must be deleted as well..(but always stop it first of course)..