If you've actually been hacked you want to get your data off to another computer and then wipe the hacked server. You can try and run a rootkit to see if it can detect any signs of being hacked.
Before using any files from the serer, check them carefully for virus and trojans.
If you just locked yourself out of the server by mistake, boot into single-user mode and reset your password.
Either way, unplug the network cable until you figure out if you've been hacked or not.
Cool project, thanks for sharing! I wish you were doing iOS, there's still not a great SubSonic client there.
Out of curiosity, how are you doing the mixes based on a song? Where do you get the list of similar songs from?
Personally, I always use rsync for these sorts of jobs. Works over SSH so don't need anything on the server except SSH, if the trasfer gets interrupted it will resume from where it left of. Overhead from SSH is pretty minimal, but if you really want thigns to go as fast as possible, you can setup an rsync server ...
If you don't want to use rsync, just use SFTP or SCP.