I have the same problem, my solution is using the devcommands just so I can repair it without a workbench so the boat can make it. It seems like it happens if you are experiencing connectivity issues between pc's. Another thing I did that reduced the frequency of this occurrence is if you run your world off of a dedicated server rather than hosting thru game directly. In this case my pc can handle running both side by side but Im sure if I had a second pc it would be much more smooth sailing.