Is it possible that the James and/or Lily Potter, in addition to possibly being spies for the Order, helped Dumbledore and/or Flamel with some kind of alchemy project? A project that Voldemort would have destroyed their house trying to find and might have killed them for in hopes that getting them out of the way would let him have access to it? I admit this may all be far-fetched, but what do you think?
This theory isn't suggesting the Potters would employed at all...merely that they were working on a secret project...perhaps, as spies, they even offered this creation to Voldemort in exchange for information? I don't know...now, I'm really off on tangents!
Anyway, like Grindelwald, I think Flamel was mentioned more importance than just as someone who helped create the Stone with Dumbledore...