BitTorrent creates a hashes of your file. The file is broken down into certain size chunks and hashes taken of each chunk. If you already have a piece with a given hash, you won't download it. If a hash differs, it'll be transmitted. The receiver verifies the hash. If it fails it re-requests that piece.

I assume the sync protocol works the same. It hashes the file, checks if any chunks have changed, sends the hash meta-data to the recipient, who then requests and pieces that have changed.