The devs are slowly dealing with this with a new system they recently started using. Most small cities are getting deleted, while larger ones are getting archived and removed from the map until the day they may come back and log in again, instead of the current system, where the larger cities sit there forever.
But in general a city will get deleted if the player does not reach, or complete, chapter 3, I can't remember which. and if the player has never spent purchased diamonds in that city or it will never be deleted. It would have to be one of the ones archived.
And the old deletion time for the small, no-diamond cities was a month since last login, but that may be getting sped up with the new system.