There's definitely two realities in play now, not a strange notion considering that we've know there were at least two all along, the Mirror Universe being the other. So why not three, or three trillion?
My hunch is that the writers do intend for the new timeline to "self repair" it's way back to the original, just based on the dialogue they've written that points in that direction. Will that mean that they've merged, or simply that we have two realities that are now identical, but still separate?
Since Star Trek has contained a multiverse ever since the MU was introduced, I say they'll still be separate. Simply because they're similar doesn't mean they need to be the same. There's probably a reality out there that's the same as ours except for the flap of one butterfly's wings, and it's still a separate reality regardless.
As for what reality we'll see in the post-Abrams-movies future, well, on TV that means CBS is in control, and I wonder if they'll even care about this stuff and what Paramount established? if Bob Orci is in charge of the TV show, he'll be more likely to stick to the Paramount scheme of things, but if Bryan Fuller or Seth McFarlane take over, who knows?
Its possible that we won't be able to tell what reality the new TV show is in. There could be a Vulcan, but is it the new colony, or the old planet? If they don't tell us, we won't know. Not telling us is the simplest way of solving the problem.
