when you build a type 4 governement and have the city ruled by a FM, it can happen, that when you withdraw this FM from the city, the city "disappears". What i mean is, that it becomes transparent on the strategymap, as if it was not your city. You still can click on it and build stuff etc., but if you want to see it "lighted up" like your other cities (incl. stuff like the visual display where you see that something is built or recruited in this city) you have to move a spy or a unit of soldiers near that city.
here's an up-to-date example from my Hayasdan Campaign (EB 1.1)
https://img509.imageshack.us/img509/...ostcitywt9.png