I have a map kill all. The big monster that shoot fire-worms, was almost killed, walk behind a building and vanished. Cant finish the mission;)
They, Chirons, vanish (go to map edge and evacuate) when heavily wounded. Mission don’t end probably because there is worm somewhere
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Ah thx Yokes 
Some others, tritons i think, can “stealth” after being shot - reappear if they move or you get next to them
Enemies can escape when they reach edge of the map. Shoot a pincer of the crab and see him run away to the closest edge 
But in that specific case, you most likely have a bug where enemy is either stuck inside of something or maybe felt under the map, restarting won’t help. You have to either regenerate mission, by loading save before Exploration or by winning by typing ‘win’ command in the console if you can’t find “last enemy”.
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