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I just had this same issue. I didn't explore it as deeply, but I did try to build a new raft (to no avail, nothing to build off of). Not sure how big the map is and how feasible it is to swim to my old raft.

I know I'm not the only one. This will go viral soon because I think almost everyone has this problem.

So I randomly swam around and by some stroke of dumb luck found the giant raft. As I was like, 1 minute away from hopping on to it it suddenly disappeared, along with the nearby island behind it. Uhhh.....