If you can monitor the FTP server's xferlog log file, that is simply the best way to ensure you don't process incomplete files. The FTP server only makes an entry in that log file when the file transfer is 'finished'. In addition the entry notes whether the transfer was c=complete or i=incomplete. In my hacked-together monitor program I can check and process only finished transfers, which were complete, and whose path matches one of several possible directories being acted on. And react so fast that remote users sometimes re-transfer the file two and three times wanting to be sure it really did disappear "on purpose". (sigh)
I've not had to use the features for renaming files that wjw mentions. Though if you can't see the xferlog file that would be a very good way to do it. And, yes, we use ProFTPD also for its extreme flexibility.