Get together with the other parents whose kids have the same problem and go over the head to Admin.
In a group if possible.
If THAT doesn't help, raise hell with the school board.
Elected officials tend to value voters, especially voters who are willing to be blabbermouths about how they were treated. Sometimes being a blabbermouth for the love of your child is a good thing.
Write letters to the Chairman of the School Board, and the School Board members with copies to anyone else pertinent in this. Detail as simply and clearly as possible the exact sequence of events that led to this problem and stay focused. If you cannot get satisfaction from each higher-up you contact, go a bit higher with the same focused letter of complaint. If there is a formal complaint to be filed, maybe that would also be an option. If you voted for someone in this group, tell them and let them know (nicely) that you expect them to do their job. (Be sure to keep a copy of this complaint letter so you will not have to write a different letter to someone else later.) It was not your fault nor was it your child's fault about the juggling act the school administration did to your child. They are acting like your child lost records that would appear to be their responsibility to keep track of and penalizing her for their own carelessness.