So, I took a look at Post Collapse. Looked around in the scenario editor. Looks like the map generation settings produce no ore, biters, etc. So, outside of the city doesn't really exist as a playable area. Also, anything deleted will regenerate the same as the barren word. I am not sure why much of the city gets deleted. I expect that not it's not all set as player owned or player force owned.
I think that if you used something like ChangeMapSettings to alter the settings for newly generated chunks then explored a new area outside the city it would work. I could dig a little deeper on why some of the placed entities don't stop a chunk from being deleted however some areas in the city would be deleted regardless for lack of entities or paving. These would regenerate with whatever settings are active and won't match the hand painted map from the scenario.