Eww, that sounds nasty. I would definitely go back to a previous save, no matter how much stuff I lost. The worst ship bug I've encountered involved the game rendering one of my coolest ships unusable - wouldn't appear on the landing pad when I switched to it, and I couldn't work around it. If I tried to fast travel to it, the game said fast travel was unavailable. Just ended up selling it.
I'm up to 107 now and I'm about ready to start over. I may go the NG+ route, simply because my accumulated skills are as important to me now as my stuff. I've got pretty much all of the useful ship skills maxed. I absolutely loathe the Guardian ships, but it wouldn't take me much time to get a different one, and I now know how to turn even a Class A ship into a death machine.
Regardless of the route I go, I think next time around I'm going to try to focus on outposts now that my understanding of how they work has moved somewhat above rudimentary.
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