No, if you have scouted a region and a player settles in it after that, you'll be revealed the city's location if it is in the already discovered part. like:



(Rualle had been scouted before, and became inhabited, I would prefer the settlement not being shown until I have actually encountered it with a unit.)



I'd suggest you give the region a color, as it is now - but hide the city until you have re-scouted the region.