If not, save a blueprint of said structure, and reload it.
Those chunks should be there again then, if not, they were corrupted by something.
You can see the difference by trying to build in them.
You get an error when they are "waiting to load" (indicates: the blueprint has marked them occupied, but no data for them), however if you can build there, they are just empty now, and the corruption is already in the past.
I got the same problem here. Cleaning the cache had no effect whatsoever, and i'm not really computer savy. Could you give more info on own to accomplish the second advised solution? I'd really like to be able to save this game as there was many hours invested in it...
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