There is no way that i know of to undo this kind of damage. You will have to start over. However a bit of good news. Only the areas that were loaded are going to be affected. Anything in chunks that are too far to be loaded will still be intact when you reload in 1.12. Unless your nephew moved around. You should be able to rebuild.
If there is too much missing you might just need to start over.
Just remember to start keeping backups.