Although it does seem to be a bit like it was your fault that your ship is gone, I felt like a good person today. So I tried to remove your other active ships from your file - with no success. Deleting the others somehow set the Casstech C14 to your active ship, albeit there being no more mention of it in the save file.
I damit defeat since I also have clearly no idea what the fuck I'm doing.
Oh, but here's another thing: The game has an easy mode that's so easy that it almost feels like an insult. You probably will never feel the need to give your character comically high stats or random perks when playing on that mode. And there's also a build in ingame cheat menu. You can access it in the options after clicking the dot in TiTs three times when you have the main menu open.
Maybe just use those instead of permanently damaging your save files for your future characters.