Is she registered for the class and receiving a grade? If so, then it should appear on her transcripts as a high school course. If she is not registered for the class, then I would start with the high school guidance counselor and ask about it. Then, I would go to the district office and talk to the person in charge of gifted.
These days, most schools have electronic grade books, so I am guessing that her name must appear on the teacher's roll or she would not be able to get grades. If that is the case, then she must be listed as a student in the class and it would be available to be on her transcripts.
My DD is in gr 7 and taking algebra 1, a high school course here, and is getting high school credit for it because the law requires that if she is in the class she has to be registered for it because there is a state end of course exam in it.
In fact, that was one of the reasons they tried to get us to keep her out of the class - "if she does poorly it will be on her transcripts and her chances of getting into college will be affected."
I would push for the high school credit because it may be a graduation requirement and you do not want her to have to take it, or any of the pre-requisites again just to get it on her transcripts.