My personal experience is that storing/archiving in FLAC was NOT a good idea, but a lot of it was because I was/am a moron (no hate for flac here). If you made FLAC FFPs when you made the flacs, you could verify them. Otherwise, I think the only way to tell if they are toast or not is to try to decode them. If the discs are discoloring, I'd save the content now if its not too late - its only going to get worse! Keep the discs out of light when you store them!
I know you are talking about going from disc -> HD, but for people who are going HD -> disc, I strongly urge them to use any kind of burning verification w/ the burning software, as well as md5s. I used to think that doing a verification was a waste of time, but when many of my flacs on disc turned up toasted, I began running verification (per advice from Skalinder). It took only a matter of seconds to see that neither the CD Burner, or my DVD Burner were burning discs that were passing verification (which was probably 1 source of my problem, in addition to a bad hard-drive). I now have about 30 DVDs with flacs on them, and I have no idea which ones are decodable or not - and it pretty much blows. So learn from my experience.
Good luck.