You might want to consider requesting the school put a 504 in place, for medical reasons. The fatigue is a direct result of the PANS/PANDAS and the school needs to accommodate. We've been down a long road with our schools. Or, if you think it's warranted, ask for an evaluation for an IEP. These will afford some protection for your granddaughter. And a good idea to build in some protections for flares--symptoms will increase and therefore greater difficulty to be in school and attend to school work. (You can ask for shortened school day, ability to leave class whenever necessary, pass to guidance office, check-ins with school social worker, preferential seating--not sure which of these would be helpful.)
We had our town truancy officer threaten us when we first began down this road! It's not fun to have the school breathing down your back while you're preoccupied with your child or grandchild's health.
There are online schools now too...