Okay, so if you haven't watched the movie The Prestige, I strongly advice you to. To avoid major spoilers, I suggest you stop reading this theory right now if you haven't seen it.
For those of you who have seen it, you'll remember that it involves quite a bit of cloning, as well as teleporting. When we see the Island move in the season 4 finale, we see that the island disappears, but no proof that it actually disappeared as in it was moved away from where it was. It could have sunk.
As we see in The Prestige, when Angier uses the Tesla-machine for his literally magic act, he gets cloned. One Angier falls to his death beneath the stage, whilst another is teleported above the audience to receive his applause.
Now, what if the island has this feature, and one Island drops to the bottom of the sea, whilst another Island is moved to another place in space and time? This could in some way explain why the Island, or one of them, was at the bottom of the sea in the season 6 premiere.
Quite far-fetched, but worth a post. Thanks for reading.