If I remember correctly, any city that has not completed chapter 3, and you have not bought diamonds, in about 30 days after your last login it will be deleted. And if you accidentally log into a server/world and a new city is started, but you never go back, those can go away in as little as a week or two.
So once you get complete the Advanced Scouts at the start of chapter 4, or if you spend money at all in that city, it should never be deleted. Unfortunately, this is why the servers are clogged with so many dead cities that have not been logged into for years.