If they..
Will run enough to charge your batteries crawl to port that way. come up charge go back down and repeat. I have had to do that when running on fumes to refuel. But if they want run at all and you are actively telling your damage control team to fix them then yeah you may need to reload to last save.... Its happened to all of us.
I know its not REAL but I try and save after or before each patrol spot incase I do something stupid like take on a merchant with deckguns and forgot to look and see if he had some himself.
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