Trek has no true multiverse in the modern sense of the concept. It's more of a single-timeline with occasional aberrations. It has the occasional "alternate timeline", but almost always uses the concept that those are temporary and collapse once the "real" timeline is restored - unless some important event or other metaphysical technobabble causes them to remain stable.

The only major examples of timelines that didn't seem to vanish after the protagonists had left are the Mirror Universe and the Kelvin Timeline. There are little pocket loops here and there, but by and large it seems that there is One True Timeline that can be reshaped, but doesn't branch endlessly.

That said, you gotta figure that the Mirror Universe version of Tuvix got wind of the plan to split him in half and did some splitting of his own.