How much data are you talking about? While it may not be very elegant, and it could be vconsidered a waste of bandwidth, it may be feasible and reliable to connect to the FTP server, turn off prompting and doing an MGET of all the files.
Alternatively, you could write a short script to connect to the server and get a list of files, then iterate through the list and see which ones are not present locally and do GETs of them.