I would think there would be a way to change your ftp program so your files get uploaded to your domain instead of the home directory. This would certainly save you a step in the future. If you are able to do this, you could just delete the uploaded files and reupload them. Other than that, I think Mattail is correct about having to use telnet.
Telnet is a very weak subject for me. Do you happen to have a link to all commands with small explaination that DH will accept? If not, maybe something you would like to add to the DH wiki.
Just a thought,