Should your file transfer be interrupted, simply go to the server and see how many images have transferred. Delete any files that were actively transferring (as the files will be truncated, and can usually be identified by their unusually small size). Then initiate a new transfer beginning with the next file to be transferred. You do not need to restart your transfer over from the beginning.
If you are using Transmit as your FTP software, you can use its convenient sync function to automatically upload all missing files.