The SOV died in the city. I don't recall seeing an AI ever flee.

Even though he died defending the city he still had other cities at his disposal. The save game has my army parked right out his city so in 1 turn it should fall if attacked. Everytime I load it and attack the city killing thier SOV it says the empire fell on the turn notes and the diplomacy screen no longer shows them. Yet the other cities they control remain.

I went back and took some Screenshots to show what I mean.

Before I attack you can see thier SOV in the city.

And they show up on Diplomacy

Combat Results

It says their empire fell yet I can see 2 other cities remaining.

And they no longer show up in Diplomacy