I'm not sure about renaming FLACs creating errors with the related MD5s...
However, this whole thing issue can be eliminated with the creation of WAV MD5s to go along with SHN/FLAC sets. Once the conversion to wav is done, check the WAV MD5. Who cares what the original format was or checking it etc., if the final WAVs check out, then its all good right???
I've thought about this and found the no MD5 for FLAC a minor issue (no way to tell if your FLACs are same as original FLAC siles except by physically reading each FFP, or using a home-made GUI. Sure, the FLACs may be error-proof, but I can EAC>FLAC an audio and make it error-free - doesn't make it the same set as the original. I think MD5s give a quick and easy way to differentiate between sources.
However, if you make WAV MD5s, then we're all good... I've started including them on all my archives...
Terry Watts