Yes, the time shifting has me really confused, I don't think they moved the island (per-say) just it's location in time/space. I wonder if the island is Atlantis or something?
I'm just wondering why they all have to stay on the island why is it so important that they stay, it must have something to do with events that unfold if they don't.
Des and the pilot, ive got no idea, but I'm sure they are alive, I also think the others on the boat are alive, that person that appeared before it blew up must have moved them somehow.