I've thought all season that the side-timeline was an epilogue after the coming fight. It's turned out to be an actual, concurrant alternate reality, but I still think that it will be the one the Losties end up in.
I agree though that Desmond and Charlie remembering their life on the island is a big can of worms open. Des seemed pretty determined to show the 815ers what he had seen at the end of the episode, so I can see the other Losties gaining their memories.
I hope that the side-Losties don't decide to reverse the actions of the nuke going off. I'd find that as silly as them wanting to set it off in the first place!
The new timeline is much better for everybody, and I can envision the island-Losties fighting to protect it or some such.