There is no reason for anything that has happened in Star Trek 2009 (now called the Kelvin Timeline) to invalidate anything that has happened in the Prime Universe. The differences between the two are supposedly the result of utilizing the technology of the original timeline at an earlier point in the Kelvin Timeline. The original timeline is unchanged.
This new universe is a parallel universe, decided different than the Prime Star Trek Universe in a number of ways. Canon from the Prime Universe will remain canon, within that Universal framework. In the new Universe, a new canon has now been established and will likely grow from this point forward.
Star Trek 2009 is connected to the Prime Star Trek universe by the event that carried both Nero and Spock Prime to their early Alpha Quadrant. But there are decided differences between the two universes both in terms of look, style and equipment differences. 3 things came to mind immediately while I was watching, there were likely to be others noted by other sharp-eyed viewers:
- The building of Enterprise A on the EARTH's surface. In the Prime Universe, Federation starships were built in space at the Utopia Plentia shipyards above Mars.
- The firepower of the USS Kelvin that's under attack by Nero in the opening sequence was far superior to anything that would have been seen in the TOS Prime Universe on a starship of that class. The USS Kelvin was bristling with phaser arrays and performed point defense maneuvers never seen before. It was also festooned with escape pods, a feature I had never even known a Federation ship to use, let alone have as many.
- The third noticeable difference is the Orion female room-mate of Uhura. At this early point of Federation history in the Prime Universe, the Orion's were barely even known, let alone members of the Federation, let alone having female members apply to Starfleet.
While the two universes may be considered parallel and connected by the Spock Prime and Nero events, there were enough differences to be noted, even if in the overall scheme of things they do not change the flavor or tenor of the Star Trek Experience.
Speculation: I did ask myself when I saw the bristling firepower of the USS Kelvin what was THIS Federation or Alpha Quadrant like if a Federation ship needed the kind of weaponry the Kelvin displayed? I suspect J.J. Abrams may have been ensuring if they wanted to show a more "warlike" or "combat-prone" quadrant, that he had already prepared us with the awesome firepower display of the USS Kelvin.
On the other hand, later in the movie, Nero was attacked by other new Federation ships and defeated them as handily as it did the Kelvin. So then I had to ask myself, why weren't ships like Nero's swarming all over the Prime Universe's Federation if they were as amazing there as they appeared to be in the new Universe. I was not sure if anyone noted this discrepancy but me...