To my regret, I separated challah, wrapped it in foil and then never burned it. It may have been more than a year ago! In my fridge I see that the bag looks like it may have quite a bit of mold on it. What should I do at this point?
The fact that the challah has some mold on it, will practically not change anything, since the kohen is not able to eat challah nowadays. Therefore you can do to the challah whatever you would ordinarily do to the challah after it is separated.