Everything that happened, still happened. The history isn't going anywhere. I imagine you're now experiencing something akin to what someone who was born in Atlantis and survived the catastrophe might've experienced. Or Pompeii. Or Native Americans. Or being sold into slavery after Carthage was defeated (sans the slavery aspect). Or any populations the Assyrians/Japanese/Soviets/Nazis/Romans/some-other-conquering-power forcibly relocated.
The islands aren't disappearing from time and space, just space (in that they will be underwater instead of above water).