If minors' special Buildings are going to be scrapped if the system is conquered, will the same happen to the empires' special Buildings? Say if the Jalanda Forum is destroyed, the Imperial Senate should be too I guess. Or will the Senate give its Morale EW bonus to the conquerors?!
-1 Morale Buildings, Native system Buildings, conquering "Conquered" systems, ...

There's a "CaptureResult" property on all building designs that specifies what the behavior should be, e.g. destroyed on system capture.