Except that how do we know that the Prime universe doesn't vanish from the memory of the multiverse immediately after the Narada and the Jellyfish are swallowed by the red matter singularity?
Mainly because nobody wants
it to. This is fiction, the rules of time travel are whatever we want them to be, and there's no reason why anyone would desire that to happen.
If you want in-story evidence, for one thing, we've seen several time travelers from the future who apparently consider the Prime universe to be part of their own history, such as the Vorgons and Captain Braxton. For another, as I said, the fact that Spock Prime is making no effort to "restore" his own history strongly suggests that he doesn't consider it to be in danger. Non-canonically, the Countdown
comic showed the TNG crew continuing to exist after Spock and Nero fell through the black hole, and Star Trek Online
shows the Prime universe continuing into 2409 and beyond.
Per the temporal model I constructed in Watching the Clock
, a timeline created by time travel can only overwrite the original if the exchange of matter, energy, or information between them is two-way. For instance, the Guardian allowed people and information to travel both ways through it, as did the transporter time warp in DS9: "Past Tense." But since Spock and Nero fell through a black hole, we can assume the exchange of information was only one-way; thus the conditions for reconvergence do not exist.
Although sometimes two-way exchanges can potentially be stable too, as in the "Yesteryear" case, which I touched on in Forgotten History
. Again, by all rights a stable coexistence should be the default
outcome, so it shouldn't need a special explanation. Convergence should be the more exceptional outcome. It's just that we've been conditioned to expect it to be more common because fiction is biased toward situations of greater danger and greater exceptionality. (For instance, one assumes that holodecks rarely malfunction, otherwise they'd never keep them in service; but the times they work normally aren't as dramatic, so the storytelling is biased to emphasize the times when they go wrong. But that doesn't mean it's necessary to explain an instance where a holodeck doesn't malfunction.)