This is a tough situation, and there's no good way to solve it. you could try wait to take the mission until the govt take the city back, but that might not happen tho. Or you could take the city for yourself and hope the govt sends a patrol to take it back. This has only happened to me once, and it was a long time ago. i think I loaded an older save before the rebels took the city and was lucky that the rebels didn't manage to take the city on their second attempt.
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