If she is stuck like that I would recommend, if you have access to a round pen or fenced in arena, to do join-up with her. So she submits to you and then she may be more willing to listen to you aids and pay attention to you while you are riding. It is easier to get her submissive on the ground as you can push her more.

I feel you pain about the fly allergy, my mare is allergic as well and will break out in hives if she gets bitten. She wears a flysheet and fly mask whenever she is outside during the summer.