Unfortunately Mr. zerow, this won't work for FLACs
You can completely remove extension from MP3 file- and it will still be playable in [probably] any player [that plays MP3's]. But if you change extension of a FLAC, that file after loading up to a player simply cannot be played
Mr. zerow, this guy just proved you wrong: Can't copy some unusual TRACK tags from MP3 / FLAC to WMA
WMA is no good for you; choose WV instead. It doesn't seem to have issues like APE and WMA do