Most likely, it will be treated as one case with 9 separate counts. You can ask the court to add your daughter to the criminal protective order, and most likely the court will do so.
The district attorney's office will decide what charges to file and how many they will file. They could file all or nothing or somewhere in between. If more than one charge is filed it will be one case not multiple cases. You would need to contact the DA's office regarding the criminal protective order. They will request that the court issue one and who is on the order.