They still happened, they're safe and sound and that timeline is still continuing merrily along in theory.
Orci & Kurtzman are using the multiverse theory of time travel in which you're not travelling to your own past but rather to a past in a parallel reality. If that reality happens to look like your own (and given an infinite number of parallel realities, a lot of them will be extremely similar just as a lot of them will be wildly divergent) then you might be fooled into thinking that you're still in your own reality.
This type of time travel doesn't rule out the other type that Star Trek usually goes for - single-timeline travel, where you really are in your own past or future - but it's possible that Star Trek characters have never travelled within their own timeline. The Grandfather Paradox holds that this type of time travel is impossible, so maybe it's never really happened?
Since they invariably "fix" whatever went wrong with their past, and everything is fine when they return, how do they know the timeline was ever frakked with to begin with? Maybe they just visited another reality where the timeline was naturally different and therefore appeared to be messed up. They weren't fixing their own timeline because it was never broken. Maybe they didn't do anything to the other timeline, either. It was all just a delusion on their part.
But since that makes jokes out of a lot of episodes, I doubt that was the actual intent. Instead, we're talking about two different methods of time travel, one of which (Trek XI's) is time/space travel.
