Was playing with some friends in multiplayer, i am the host.
All of a sudden one of my friends start seeing our ship as the state it was in a few weeks ago. Relogging did nothing, only closing steam and restarting the game worked. Later this even happened for me the host, but my friends were still able to see the ship, and interact with chests. I decide to try and restart the hosted game, and when we logged back in, all of us had the old ship.
The bug started happening once we had explored some caves and had unloaded the ship. Hope this helps you in some way.