Since this has been posted everywhere else but here, I will post it here. The community on steam and here has checked into this and it is a thing. Including /force_saving just before exit, at a full stop, people are missing their ships when they log back in. 10 or more people at least have reported this through various community threads. I am positive that many more rage quit and will never return when their ship went missing.
This is a singleplayer issue. The server is saved and stopped. Searching for the ship provides no result.
This is a singleplayer issue. The server is saved and stopped. Searching for the ship provides no result.