If you haven't watched "Happily Ever After", the eleventh episode of the sixth season of "Lost", you might not want to continue reading. Spoilers ahead.
So, a few characters in the alternate timeline are aware of certain events from the "regular" timeline. Desmond, meanwhile, seems like the only one in the "regular" timeline that is now aware that somehow time split in two. This means that there is an actual connnection between Regular Time and Alternate Time.
Before this episode aired, I read a few people theorize that we're seeing an epilogue in advance, where the Alternate Time is the result of something our heroes will do in the finale. One of those people is Alan Sepinwall, who has now abandoned this theory. I don't think he should. I think he was right about the "epilogue in advance", except he looked at the wrong timeline as the epilogue. I think the Alternate Time was the result of the nuclear explosion, and the Regular Time, the one with Fake Locke and everything, is the result of Desmond, Dan Widmore (as Alt-Faraday is known) and others counteracting the nuke somehow, and returning the original timeline to what it was.
Faraday always said that whatever happened happened. No matter what, I think things would work the way they did. After all, if the Alternate Timeline stood on its own, there'd be a paradox with the Losties never going back in time to set up the bomb in the first place, so it is inevitable that the Alt-Losties will somehow restore the original timeline.
This theory doesn't explain everything. How did Eloise and Widmore survive the nuclear detonation in the Alt-Timeline? Since when is a nuke capable of drowning a whole island? What is it that Desmond think he needs to do now in the regular timeline?
We'll see if I'm right soon enough.