Sylen’s got the technical answer, but it does beg the question if the game should work this way. I’m with CoinSpin: seems like an oversight that’s never come up in formal testing. I’d file a bug on the official site - it should be an easy correction to make.
There really isn't a way. It had nothing to do with using godmode/dev tools to do the demolition.. It's just that the game pre-generates a POI map for long distance viewing at world creation, and then when you are far away, it refers to that map to show you what is, or was, there.
The long distance pregenerated file is not updated at all post creation, so any demolished buildings will remain visible at a distance and vanish when you approach and load in the actual world. (Likewise, the long distance view will not incorporate any changes to the POI or it's surroundings.)