Why does it need to be a continuous process? It would just be a fraction of saved multiverses, a fraction of destroyed multiverses and a fraction of multiverses that were not susceptible to that particular destruction mode, some of which get destroyed via some other mechanism.
If you're using multiverse in the sense that physicists do - which is what I thought they were saying at the time - it means it contains all possible universes, everywhere - whether that is a finite or infinite number. Hence, the multiverse can only be destroyed once. The logical conclusion of this then is if there are an infinite number of universes the multiverse cannot be destroyed, because there would have been an infinite number of chances earlier in chronological history than the present for it to be destroyed (if it even makes sense to talk about time flow when comparing individual universes).
That said, it does strike me that the writers might have been using "multiverse" in an inexact way, referring to Prime, the MU, and a relatively small number of other universes, not the whole shebang.