Well… if I were you, and interested in the idea that going back and re-doing something would eliminate other universes, I would try exploring that situation and others in fast-forward brain-storming mode, to see if you like the results or not. That can help you decide how you want it to work in stories you’ll want to write, or not.
Personally, I don’t follow you, and would tend to think it’d work differently, but I suspect you may have various alternate ideas about the ways parallel universes work, compared to what I have seen done, or things I’ve imagined myself.
In particular, you seem to be saying that going back in time means the traveler returns to their own body and timeline at that time, but apparently brings something different with them from the future which can change what they do. As opposed to, say, Doctor Who or Star Trek time travel, where going back in time means your future body arrives as it was in the future, but now interacts with a past situation, including, potentially disastrously, meeting one’s past self and possibly creating some sort of paradox, changing the timeline you were familiar with, changing you, having your future self suddenly not exist, or whatever.
The question of how many universes exist, and how many timelines exist per universe, and what happens when people travel between universes or timelines, is interesting and significant, but the truth so far seems to be that we don’t know any such travel is possible, nor what effects it would have. That leaves it up to the author but the implications of saying it works a certain way are often so complex and non-obvious that many authors say it works one way, and try to think of implications, but end up either not explaining or not thinking them through well enough, so that many in their audiences become confused, frustrated, and/or have objections due to paradoxes, complaints and/or implications that the author doesn’t seem to have addressed to the audience’s satisfaction. Etc.
For example, in your limited example above, if the “multi-verse” supports at least three different universes for three different reactions of one single person in an ordinary (ok, dramatic) situation, then I’d tend to think ( / hope) that one person traveling back and doing something else different, would just result in more threads, not in erasing existing threads. So I would expect that after John did his thing, there would still exist somewhere several threads running:
1) Main narrative thread: John made a choice 1 at event A, then traveled back in time to before A, makes a different choice at A, and is now living out that thread.
2) John made choice 2 at event A, and did whatever after that.
3) John made choice 3 at event A, and did whatever after that.
I would also expect:
4) John made choice 1 at event A, then used a time travel machine to leave this universe thread, which now continues normally but John is gone from it.
Now, threads 2–4 may well be inaccessible to John from thread 1 after he travels back, or not, but it seems astoundingly egocentric to me to assume that time travel causes universes to vanish, or everyone else’s futures to disappear. They might make then irrelevant to you because you’ve taken a different path yourself and you might not able be able for your consciousness on this thread to go mess with those other threads, but I’d expect them all to “exist” if they existed before.
But you could of course make up a system where it worked that way.
I think a common pitfall (in terms of making sense) of time travel genres is that they want paradoxically incompatible things: they want to be able to have their main characters travel between universes and change things, but they often also want that to be highly significant for the rest of the universe or even the multi-verse. But even our planet has billions of humans and thousands of years of history, and even our one galaxy has a practically incomprehensible number of stars, never mind the incomprehensible number of galaxies in the observed universe just at present. If every decision by one person can “create another universe” timeline branch, then it really seems like it would be infinitesimally insignificant to the infinitely varied array of timelines, if someone messes with a few of them, since apparently every time someone makes a choice, we get more universe threads, not fewer. And even if it were possible, as in some sci fi, to cause whole timelines to change and not exist by traveling back, then it’s something of a losing game, it would seem, to even try, as eventually more people will loop before you existed and cut off your story and have it not exist, which is pretty much the opposite of having significance in a story.
Seems to me like the rational response to the idea of an infinite array of universes is to try to be in the most enjoyable one, not to try to control all the universes.