M.M.
It really sounds like stress. High school can be so hard socially, especially if you don't know anyone. It seems like everyone has a "group." The good news is, because it is early in the year and she is a freshman, the groups from middle school will start breaking up and reforming into new configurations with the new people (assuming her high school takes kids from more than one middle school). Maybe you can encourage her to talk to someone in one of her classes to start up a friendship, or you can reach out to other homeschool moms in your area and see if there is another student in the high school that is coming from a homeschool situation -- then arrange a lunch date or study session?
For the immediate stomach stuff, I'd see if she will take baggies of small food like almonds, Cheerios, cheese squares or even peppermints. Anything she can get down while she is there. Even if she just sneaks a few bites here and there throughout the day, it may help get her on track. Possibly even a thermos of milk, if she can't eat. Milk can help with any acid and also fill her up like a food.
Good luck!