Okay, long story short, hit a rock in a storm, had to put into shore for repairs. Dark forest. Of course there was a Gray Dwarf welcoming committee. And the noise of fighting them brought a Troll. So I ran off into the forest to hide. Snuck back just in time to see him smash my Karve to splinters. Now, I saw the wreckage and the cargo crate. Hid in the woods until it stopped raining, and once I was rested and my Eikthyr power recharged, I went back in daylight.
Nothing. Not a nail, not a scrap of wood, nothing. Had her beached in shallow water, too.

I have left cargo crates and bodies for a long time, and they were always right were I left them. I haven't slept in the game, so that's not it.
Has this happened to anybody else? Or should I report the bug?

Problem is, I think the island I'm on is entirely Dark Forest. And all my Fine Wood that I need to either build a new ship or to build a portal went down with the ship. No birch trees- no Fine Wood. I can't even build a raft without boars to hunt.
On the plus side, I haven't set a spawn point on this Island. Last place I slept was in the meadows, so I can always respawn there.