What OS is the FTP server running?
As you could SSH into the machine and manually (through the command line) do what you want to do, if the machine is running OS X or Linux.
Also alternatively is the possibility of Remote Desktop (Windows), VNC (Any OS), or Apple's Remote Desktop (OS X only).
Between those 3 you should be able to get control over the machine and do the changes you need to from wherever you are. However, be sure to choose a very good password.
I still remember Macnutt.