DevoRevo
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To understand which of the Hole tiles need to be removed, it is enough to know the location of the center. Finding the center is very simple: in the Objects Properties Tree, find Pos => + => Set any coordinate, press Enter. Then, look at the city from above, hovering over the cell with the same coordinates: the cell located at the coordinates specified manually through Pos is the central one.
It's easier to remove all Hole Tiles and then add them back if needed, or to create a new city instead of modifying an old one.
Is there a guide on how to create a new city?
I copied the Shared graph and worked with a copy of one of the existing cities, but for some reason, the hero couldn't enter it (the icon to enter the city was not displayed), although teleporting to the city and exiting it was still possible.