Ok it has to be like this:

I landed the boat at the Swamp coast. Boat was ok then.

I built a bed and workstation at the nearby crypt entrance. The boat was slightly outside the workstation radius.

While I was in the crypt and also in my house (by portal), the boat might have been destroyed by monsters. Materials despawned then.

So, the learning is: take the boat materials and put them inside the Worksation radius.

I would not have expected the boat parts to despawn so quickly.