In my case, the combat was not related to fighting in a quest.
1. Destroyed an enemey outpost near my borders,my city dissapeared.
2. Reloaded previous save. Instead of destroying outpost, I attacked some trolls, same result, my city dissapeared.
3. Reloaded again, didn't attack anything, and my city remained. Later, I took over an enemy city, nowhere near my dissapearing city. My city dissapeared again anyway.
After the 3rd dissaperance, I also happened to notice that the tile where my city dissapeared from no longer had the food/material resources.
Here is the link to my seperate thread, which has my save game, debug, screen shots, etc. Figured I'd post it here as well, since this is the largest thread with the same issue.
https://forums.elementalgame.com/416860