Sorry for the late response! I really, really like this theory because I hate the official stance of the Heroes universe:
A question on the universe that “Heroes” takes place in. Is the universe a multiverse, like the Marvel Universe or the DC Universe used to be? Where futures are all probable and stemming off of a main universe, where there are multiple realities, some with slight changes and other with many changes from the others? Or is it a single universe, more like “Quantum Leap,” where the changes are retroactive but the only ones who remember the differences are those involved?
Yes. That one. Single universe. (x)
Which sort of implies that Caitlin no longer exists, because if there’s only one universe, there’s only one timeline, and the one with her “doesn’t exist anymore” (x).
For Caitlin fans, I remind you that the writers have totally gone back on their word before, and that the continuity in this show sucks, so feel free to believe whatever you want because authorial intent is meaningless.