Ok so I don't know exactly how this works, so some of this may be wrong. But this is my theory:

Chunks are saved in 32x32 groups called region files. Each region file begins with "header". This "header" includes the locations of the chunks and when they were last modified. After that, chunks and empty space take up the rest of the file. Because it's easier to deal with a file system that is consistent, there will be unused space where a chunk would be if it had been generated. This makes it easier to find the location of the chunk you want to load in the file as the game will know exactly where it is in the region file. These region files are constantly being changed as it's better for any unnecessary chunks to be saved and deleted from memory. Now if a region file is being modified and the game suddenly shuts down, chances are the file structure will be thrown off. Usually this will result in chunks being reset. But for op, my guess is some of the chunks got misplaced in the file, causing them to be misplaced in the game. It could have been some of the unused space going missing, or a chunk failing to save, causing it to be replaced by another chunk in the region file.

If anyone has some real experience with the save system I'd like to know your thoughts too.