Using lsof is not safe, ftp may release the file if the connection is broken an reaquire later this happens seamlessly from the users perspective. It is also not supported by all unix.

The only 'safe' way to do this is to do what merlyn suggests. However if you cant rename then you could upload an empty file after the upload is complete and poll waiting for the control file to arrive, as soon as it arrives you know the preceeding download is complete.
-- Zigster