We know the island moves. Which means, theoretically, it isn't attached to the ocean floor. So what's keeping it afloat?
We know that there is at least one "pocket" of energy deep within the island. They drill into this pocket while building the Swan hatch. Perhaps it is this pocket of energy inside and
underneath the island that keeps it afloat.
Faraday told us that the bomb would "negate" the pocket of energy. So perhaps (in the alt timeline) the blast (though not strong enough to sink the island itsefl) was strong enough to negate (or sort of "pop") the pocket of energy. With the energy gone there was nothing to keep the island afloat. So it sank.
There you go. That's the best I got.
