Based on collected data:
1. FLAC is like a zipped WAV file.
2. When a player plays FLAC its like unzipping the WAV and playing it back.
3. Converting FLAC to WAV does not affect the file because its just unzipping the WAV.
4. I'm not really sure if the compression/zipping of the FLAC has soemthing to do with it?
I think during the process of Unzipping the files is the problem to be honest.