Welcome to the clusterf*** that is the Marvel adaptation of mythology. I think we can basically assume that the gods were eating the golden apples consistently before the final Ragnarok. After that, who knows? Balder mentions that the gods are all a bit more vulnerable on Earth after one Asgardian kills another in a brawl, but no reason is given. Maybe it's because they're not eating the golden apples anymore.
As for the Enchantress' picking the golden apples, it seems like that was only true in one of the earlier Ragnarok cycles. In the current continuity, we've seen Idunn, Amora, and Freya as separate characters over the years, and Idunn was the one who picked the golden apples. We haven't seen Idunn since the final Ragnarok, though, so who knows what the deal is there?