This is in the campaign. Just got the hooks for the mantas and I was otw to stop an invasion, then suddenly my carrier was damaged and the enemy carrier was leaving. All happened while in time warp I guess.
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It does not repair the repair systems it seems. Have been timewarping to see if it repaired. Selected top priority and have full fuel. It seems like its a part of the campaign so don't get why it can't be fixed. I don't see the battle or anything. Just get a damaged carrier.