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You could build a teleporter and go to station or your base (if you have one), that way. Typically when you show up at station, your ship will be there waiting for you.
Edit: probably your best bet is to build a mini base with a teleporter. Go to station and be reunited with your ship.
Thanks for the tip; I do recall seeing consoles like this around, but I had no idea it meant my starship. But in my travels so far I’ve only found one navigation data, and already spent it. Any tips on how to find more of them, or do I just need to keep searching abandoned containers and hope I get lucky again?
Edit: Also if you don't want to lose all this game time you can find navigation data all over the place. You can buy it and find it for free at the small settlements. To find them look for the blue cubes, Round holograghic plates or the orange 3d rombus thingie. You can also find those in shelters but since minor settlements also come with a landing pad that seems the better bet. Lastly if the planet you are on has "ancient data structures" those are almost always good for nav data. Use your analasis visor to see if you can spot any.
I'd try gong to base and saving. Then get out of the game and re-enter. Hopefully the ship will spawn correctly.
Weirdness with loading terrain at your base site can happen sometimes. Usually it sorts itself out after a minute of standing around inside a base module, or reloading. Doors can disappear occasionally, as well. What you should NOT do is save your game when your base is in a messed up state, or else the loading error can become permanent.