This has confused me as well. I upgraded my ship and put a logo on her and then sailed on a mission, then I added a few mods and couldn't open that save anymore, so I started a new campaign (skipped the tutorial) and I have a noob ship again and no logo and the dock guy's upgrade options were all greyed out.
I figured when I unlocked a option or whatever it would be available to me in the future but I guess I have to unlock that stuff for each and every campaign? And what happens if I fail a mission? I'm forced to start all over again?
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