I was playing for just a few minutes this morning before work. When I came home I went to start up my earlier save game only to find that I apparently no longer have my kingdom. The screenshot below is what greeted me when I loaded the file.

The following turn I was treated to city outlines, but still nothing more on the map. It did, at this point, bring mention of a farming bonus from my agriculture research coming up, as seen in the lower right hand corner.

A couple of moves later, the sovereign is within his city. The city doesn't appear on the cloth map, but it does exist, quite selectable.

I would upload a brief video demonstration of me trying to select the city, but it came out very jittery.