Question about remaining settler in transport thing

[Kampus majore]

Many of us have heard the story of the Settler in transport thing, but for those who have not:

You have almost conquered an entire civ and when you take their last city, they still exist! They happen to have a settler in a transport (or other ship) and untill that transport is destroyed, you can still talk to them, trade with them etc.....

Now here comes my question: Can a city of that AI flip back when they have no cities?

In my last game I had this problem and to avoid any risk I destroyed the transport once I discovered it...

[Harovan]

Yes, as long as they exist, the city can flip.

[Kampus majore]

Hm, then I did the right thing to shut them up for ever!