Well there would have to be a reset since the O5 need to go back to past and forget everything that they experience in present. And they really have to end ANXM that way because the whole point of the story is that these really are the 616 versions from the past, that's the hook and if they retcon it so that they end up as alternate timeline versions then the whole idea behind them becoming to the present is undermined since they'll just be yet another bunch of alternates.
So either they need to wipe O5's memory of everything and send them back to the past or O5 need to be changed into alternate versions. Either they reset everything or pull the rug under it. They're damned if they do and they're damned if they don't. That's why I don't like it, no matter what they do it'll just end in disappointment imo.