I think you need to give her sometime and try to force to pick her up. I have a buck Netherland Dwarf and he doesn't like to be pick up too. I found that this breed of rabbit don't like to be pick up too much. Give more patient and time eventually her will learn that you are trying to hurt her. When I pet Snoopy, he would step back too, because for a past 2 weeks, I had to force to pick him up to clean his sutures, so now he doesn't like me too much. Also when he eats the carpet I force him back to his cage, so definitely he dosen't want me to get close to him. Now I don't need to clean his sutures and I learn why he was eating my carpet, I will not force to pick him up or force him back to his cage, whenever he has playtime, I would sit on the floor with him and give him treats, and he does run to me for a second and leave. Spend more time with her in her cage, like just sit with the door open, pet her, give her treats or feed her with her favor veggies, let her get to know you.
Rabbit doesn't like us to reach in to their cage much, especially for female rabbit. when you clean her cage, maybe you can try to open the door and let her come out by herself. I bunny sitted my friend's bunny for a week last month, she has the same exact problem. Whenever i reached into her cage she stomp with his back legs and bite me hard. So I waited a little and let her come out on her own before doing anything to her cage.
Right now it is hard for me to get close to Snoopy when he is running in the house, whenever I reach out my hand, he flee quickly. but don't give up or afraid, rabbit is a very smart animal and they can learn, just the matter of time.