If you get a machine uprising as an organic empire, half of the buildings on the robot occupied planets just disappear, they don't get ruined, they disappear. Also, once you get your planets back, all of your city districts also disappear. I'm pretty sure this has to do with how robotic civilizations don't use the buildings that get removed, and that they have different names and descriptions for their housing districts. This has made machine uprisings very tedious to play through, and the redevelopment you have to do after you recapture your planets sucks the life out of the game.