So i was thinking how similar the beginning of 2009 trek and TNG's "Yesterday's Enterprise" is and how both ships, the Kelvin and the Ent-D both encountered a temporal rift, a ship came through and everything changed. But to correct things, the alternate End-D sent the prime C back and restored the prime timeline. This didn't happen in the "Kelvin Timeline" and so it carrys on.
No, you're thinking about this the wrong way. The
Enterprise-C didn't create an alternate timeline by disappearing and reappearing 20 years later. It simply traveled into its own natural future, where the Klingons and UFP would be at war. (Like when Doc Brown's dog, Einstein, went one minute into the future in the DeLorean in "Back to the Future" -- going into the future doesn't alter the timeline, it just means you disappear and then reappear later, having no effect on the timeline.)
There was no alternate timeline created until the end of the episode, when Lt. Yar took the
Enterprise-C back in time, created the alternate timeline where the Federation was not at war with the Klingons, and she had a half-Romulan baby. (Every other episode of TNG took place in this alternate timeline created by Yar -- "Yesterday's Enterprise" depicted the original, unaltered timeline.) What Lt. Yar did was exactly the same as what Nero did -- they both went back in time, created an alternate timeline, and stayed in that new timeline until they died.
Likewise, in "Endgame," Admiral Janeway went back in time, created an alternate timeline by getting the
Voyager back to Earth decades earlier, and died in that alternate timeline. That alternate timeline was depicted again in "Star Trek: Nemesis," where Admiral Janeway is seen back on Earth giving Picard his orders.
Between Lt. Yar, Admiral Janeway, and Nero, many alternate timelines have been created in exactly the same way, and none of them has ever been "fixed." We just follow the time traveler into the new timeline, and continue on with the story in that alternate timeline even after the time traveler has died and their original timeline is forgotten. There was never one "Prime" timeline. This new timeline is no different from the dozen new timelines that have been created in previous episodes and movies.