I have had a conversation with a ghost unit form Kraxis. I could even initiate diplomacy and trading with the dead karavox (though I was afraid to, because I did not know what the consequences would be).
I had a similar thing happen in 1.1. I defeated a faction by taking their last city and somehow after that they finished construction of a unit which appeared next to my new city.
I could initiate diplomacy and funnily enough, the enemy would have agreed to become my vassal (whatever the exact term was). I didn't dare to try, afraid of wrecking the game.
