Object rearrangement.

Not at all. Even on the hardest difficulty, I managed to rebuild cities immediately after capturing them or almost immediately (within a day or two). What more can be said about other difficulty levels?

If you can rebuild cities immediately, it means they are empty. Consider that you are playing Heroes of Might and Magic V/III, you got lucky with the random generation, and you got your desired city :) Just like your opponent. And you won't have to restart. I still don't understand what the problem is. I thought the problem was with rebuilding already built cities...