I have a feeling we won't do anything with the medals till we either kill Isiah or just before that, but I hope I'm wrong.
If they do follow that path like say turning in a amulet or book at the end of the game either tell us we need to take medals with us before hand or make the quest/challenge repeatable because so far the major quests( riverside, temple) are not repeatable on chars so If you did the final mission theoretically and didn't know or didn't have your medals with you to turn in then you would be screwed on that char. So plzzzz Anet let the info flow and set us free :)