Just a thought, really....
Could it be that a version of the island has been underwater since Ben turned the the frozen donkey wheel? We saw it disappear--smoothly slip away as though swallowed up. The island would have gone wherever it went in tact, not blown to smithereens as it would have happened had that hydrogen bomb detonated when Juliet hit it with a rock.
I do not believe the bomb caused the island to sink, not when we're seeing the swing set in one piece, a whole Dharma house, and the foot on its pedestal, just as it looked in 2004.
Eloise said the island moves naturally through the space-time continuum, on a certain, predictable course. When Ben turned the wheel, however, that was no natural, rhythmic shift along the continuum. That was a big jerk, a disruption of the cycle.
We could see when Ben was down at the bottom of the Orchid Station that the wheel had not been turned for a very long time, if ever. It was pretty much locked in place. No wonder it caused time to skip-jump, rapidly, herky-jerky from era to era. Nothing smooth about that pushing of the wheel. Nothing natural.
And, added to all this, he wasn't supposed to turn the wheel. John was.
Due to Ben's manual over-ride, an anomaly was created. Since then, a "version" of the island lies beneath the ocean in addition to the version of the island that skip-jumped along the natural space-time continuum of the island when our characters flashed through time. One version stayed above the water line, another sunk.
Ben's turning that wheel was special, in a way. It created another reality, a separate reality from the natural continuum.
I don't believe the sinking of the island has anything to do with the war they've been talking about or the end of the world. It's just another timeline, a dead-end timeline created by Ben.
Or, I could be completely wrong!