The chicken enchilada orders work a little different than the short ribs and fruit/cheese options, since the chicken is part of the standard catering cycle loaded for the flight. The special ordered options (everything but the standard protein/veggie option pairing) are managed individually, but when catering swaps out the standard cycle for the flight, they won't have anyone's protein or vegetarian selections for those standard pair. IME, when the FA gets the note on the swap (or realizes it as they reconcile the pre-orders with plate count), they usually come around and explain the issue, list the two new options, and give us the first choice of protein or veg. I appreciate that since that's about the best they can do with what the caterer gave them.