Hmm, I'm not so sure how the FTP commands work in PHP, but I bet you'd have to find the filesize on the FTP server and then fseek() or use the FTP equivalent to offset the previous filesize in bytes.
I'll look it up on Google and post the results.
[Edit:]
Okay, it looks as though PHP comes with built in FTP_AUTORESUME, but it only works when you have FTP_AUTOSEEK enabled.
Additionally, under ftp_fput, as of PHP 4.3.0, you can add startpos, in bytes, as a position to start from.
Use the filesize of the previously uploaded file to get the starting position.