A few people have said that there's one huge-ass reboot at the end of the film and things get reset to a more familiar timeline pattern...but to be honest I have no clue. Might be true. Might not. Leaving the Abrams TREK in a slightly altered timeline lets him get away with more movies and stories that don't have to be rigidly tied to older canon and respect all the continuity of past films and TV episodes. But if an all-new timeline persists into the forseeable future of the franchise and Series #6 is based on it, then it opens up a much bigger can of worms down the road.
I hope you like worms and sausages. Here, bend over.
Ouch.
Personally, I've mentally accepted the overwhelming likelihood that the old TOS timeline now exists in a separate continuum and the new movies and sixth TV series will happen in the new timeline set up by Old Spock and Nero. It's not what I
wanted. But Paramount is determined to tweak the franchise to sex/jazz it up a bit so it's more popular with rank and file audiences, so the Abramsverse and Abramsprise seem to be what we're likely to get for the forseeable future.