If Jin is alive, he must be with the island or he would have made some attempt to reach Sun.I think he'll either swim back to the island (if he was "moved" with it)
But he was further away from the island than the copter when it did its vanishing act, so how could he have moved with it if the copter didn't?
Jin was in the water and the helicopter was in the air. Maybe stuff in the water was affected.