This is not an issue with computer files, it seems to be connected to a seed. It seems to happen mostly to caves, though trees, terrain, structures, etc. can also be affected. Whatever is generating seems to stop dead in its tracks if it tries to generate in a specific chunk. A seed will always have this happen at the same location every time. The screenshot example was taken at x=400, y=32, z=-208, and the seed is -676194426, though I have seen this occur in several other worlds and it always appears in the same place.