The World Machine can change the code of the world at will - this was unintentional at first, the squares being a result of that, but after Solstice they began to be able to control it.
Anyways, following Solstice, they began to work closer with Cedric, Rue and Proto, mostly because they're the closest people to them besides Player and Niko (and they aren't around anymore), and the children would work with the World Machine to try and reconstruct the world.
I'm pretty sure it's said that the world was built on the memories of people the Author knew, so to maintain the structure of the world, the three would go around asking people in the simulation about people they knew, places they had been, etc.
It would be a slow process, especially in areas like the Barrens, where the place is sparsely populated, but over the coming years, as the world recovered, pieces of the would would be reconstituted, and rebuilt, probably starting with the Refuge. They would then be filled with people, and the asking would continue, eventually spider-webbing until the entire world is reconstructed.
The World Machine would probably also change some stuff about the world to make it more comfortable for the people living in it, albeit subtly (or as subtle as spawning something in in plain sight can be) like placing a door or roof on Lamplighter's 'house.'
Probably just me wishing everybody has a happy ending, though.
This has been sitting in my inbox for so long without me noticing I'm sorry??













