When McCoy went back in time and altered history in "City on the Edge of Forever", the timeline he came from was erased.
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When the Borg went back in time in First Contact, the Ent-E actually saw their timeline being erased. The "doubling effect" never occured; it was always a single quantum reality that changed internally, with no "branching."
If that was the case, then how were the landing party and and Enterprise-E still in existence? They were ontological orphans, with no history creating them. Not unlike the Enterprise-E at First Contact, or the crew in 1986 would've been from the perspective of the Post-Nero Timeline. But that's beside my point. My point is that whatever arbitrary device insulated them from the changes in the timeline could just as easily be argued to have sidled them over into the new universe created by the timetraveller they were so close to.