Star Trek has been time traveling since the Naked Time. By some current theories and the one used in JJ Trek, if one travels back in time and alters it, a new branch of the time line is created. So wouldn't the Prime time line had ended in the Naked Time episode? And branched again each time they went to the 60's? An I guess earth was destroyed by the Whale probe in the time line they left when they went to the 80's.
Ah the "prime timeline". Is it the one that Kirk dies (in "Generations") or was alive when Scotty left for the Norpin colony (in "Relics") ? It's more like Schroedinger's Kirk.
I think the "prime timeline" in AbramsTrek only exists in the AbramsTrek-continuity. IIRC, Abrams or one of the writers cite "Generations" as to why Shatner doesn't appear in their movie so it sounds like they picked a timeline/continuity for their "prime" where the events of at least the TNG TV series happened differently or not at all.