I use bittorrent sync to copy my Steam (gaming) folder that is 100+ GB. Steam has multiple 100+ MB files that have the same SHA1 for various games. My suggestion is that Bittorrent sync have an option to check the SHA1 checksum of any files that are 50+ MB (or customize it) on the "source" computer, copy one of the files and duplicate it on the "targest" computer to save bandwidth and time.