Você precisa passar o --checksum
para garantir que os arquivos tenham o mesmo tamanho & vezes na origem e no destino não são ignorados. Então, conforme Wikipedia :
The recipient splits its copy of the file into fixed-size non-overlapping chunks and computes two checksums for each chunk: the MD4 hash, and a weaker 'rolling checksum'. (Version 30 of the protocol, released with rsync version 3.0.0, now uses MD5 hashes rather than MD4.[14]) It sends these checksums to the sender.