Sorry, the flac files are definitely still corrupt. The original (and faulty) MD5 data is stored within the flac's STREAMINFO medadata header, so if you have not updated the flacs then you haven't actually fixed anything.
See: https://en.wikipedia.org/wiki/FLAC
"CRC checksums are used for identifying corrupted frames when used in a streaming protocol. The file also includes a complete MD5 hash of the raw PCM audio in its STREAMINFO metadata header."
Therefore, changing the md5 file doesn't do anything, since that faulty md5 data is already stored withing the flacs.
And as