Have you added any ships to your game?
I tried to add some modded ships to the game and made a testmission. and when trying to run the mission the ships would disappear from the surface. They were simply not visible when using the freecam. When looking at the navigation map they were there.
When zooming in on them with the freecam I could see some kind of a shadow. So I guessed there was something wrong with the ships texture. Only had the problem with this one ship type which i installed manually myself.
Haven't had any problems with all the original ship, though
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