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I agree that is super annoying, happened to me in my game where they killed my fox people researchers. The fallen empire nearby instagibbed me and I essentially "lost" the game
 
Oh, just wanted to report this as well. Annoying as f***. Good thing they only purged one world ... now stuck in the never-ending bombardement of the 4 worlds they got before I got rid of them. :/
 
The Prethoryn Swarm generally seems like a pretty bugged end game crisis at the moment. You also can't wipe them out at the moment.