I'm not aware of any cities that were so depopulated that they were abandoned, however there were certainly smaller villages that this happened to. The example that first comes to mind was the village of Lidice. The Nazis incorrectly believed that it had helped harbor Reinhard Heydrich's assassins, and ordered that all the adult males be shot, the adult women sent to concentration camps, and all children were either adopted for Germanization (those that met their fairly arbitrary standards) or removed in some other form. Finally they ordered that the town be burned to the ground and leveled.

Even with such a draconian and drastic response, 153 women and 47 children returned and rebuilt the town near the site of the old one. With such determination being demonstrated in even one of the most startling examples of a village depopulated by the war, it's hard to see an entire city calling it quits.