Thanks for the clarification! Question: when you say artwork "labels" are not being preserved after the FLAC/M4A conversion, do you mean the artwork tag images themselves, or just the naming used for the images--cover, back, folder, etc?
Either way, after the conversion to M4A, what happens if you then do the copy/paste tag technique described in the wiki link I mentioned from the FLAC originals to the M4A's? Does that correct the issue?