My ship has glitched out HARDCORE. I was in the middle of upgrading it when the game quit itself and then lost the upgrade, lost the materials, lost the quest to upgrade it. I am stuck with the old tier of ship with none of the benefits and none of the ability to advance and I am stuck hot dang if someone could give me any advice here I would be so ridiculously grateful I'd probably do a dance.
which upgrade? You were not specific at all... Where are you? After first boss, second boss, a ship expansion? What shows in SAIL, in the non-mission tab? how early or late in game are you? what tier are you? (armor)
As the last thread I visited said Starbound has a useful backup system, where if the current save file becomes unusable from corruption a backup will be used instead (about 3 are saved at a time, no idea of the time difference between them though) Because of the time taken between backups, you could easily lose a lot of progress if you were progressing quickly.