It is a single player game, so not Empire take over, I think; if it *is* the case though, go to the Options menu, and save up your Empire, then edit it in a new game. That would allow you to check all the Empire values and your happiness type: if the Empire you've just taken over isn't Peaceful, you want to know it *right now*. Trust me on that one.
Incidentally, you cannot repair components if you lack the technology to do so, but I doubt it is the problem here, since it was you who made the retrofits in the first place.
Re: Retrofit Problems
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