Loaded up world, a chunk error and random deaths

Short: Loaded up world, 3 villagers disappeared, cow disappeared and a chunk appeared that was never there.

long:Loaded up my world after a week of not touching it, and upon loading up i realized a cow attached to a fence, 3 name-tagged villagers were (originally though the cow escaped until i realized the villagers were gone too (They were safely contained so were not killed) and after trying to figure out what might of happened, stepped out to find a new random chunk that formed, that never should have.(grass chunk above ground level, in a river, inside a desert biome.     

I dont know how this could be fixed but this a real pain since it costed quite alot of emeralds to trade for master librarian, armorer and weaponsmith, and now i have to remove the chunk error to restore the worlds look. 

( Image attched is the chunk error with the chunk outlines to show it is exactly 1 chunk.)