She should be able to call and request that they explain the changes they have made, and with her permission you should be able to listen to the call. OR you can get a signed Form 2848 and call and request that the change be explained to you. OR you can submit the 2848 to the CAF center, wait a week or so, and look at the account transcript on line which should explain the changes.
If they have changed her return to a refund, I am not sure why you need a 1040X to get her refund. They should send that automatically. Of course, they usually include an explanation when they notify you that they have changed the return. Are you sure thay you saw the entire letter - front and back?