OK, I've got one.

The disappearance of the Isle of Val was caused by it being displaced into the Void, possibly by means of a large-scale warping magic. By whom, for what reason? No idea. Could've been malevolent, or maybe it was an experiment that backfired. I'm interpreting "like in power to Ultima" as not necessarily meaning "destructive power." Urianger's report states the isle "ceased to be," and while the journal entry for the quest says it was destroyed, that may be only an assumption on our part.