Rabbits are prey animals. So when you are standing and bend over to pick her up, it induces a fear response because it’s similar to a bird swooping or another animal coming down to grab them. Try squatting or sitting on the floor and then trying to get her to come over to you so you can get her.
Another option is to try the herding technique. Where you herd her back into her cage without picking her up. I think you have to have a lot of time and patience and teach them what this herding business is though. But it’s an option too. Rabbit.org has some info on it. You just clap your hands or use a broom to guide them towards their cage and they are supposed to go back into their cage. I did try this with Eddie but I don’t think he knew what I was doing so it didn’t work. Which is why I think this needs to be trained.
What I ended up doing with Eddie when I first got him was attaching a pen to his cage. I’d let him out when I was home but when it was time for him to go back in his pen, I’d rattle the treat bag, he’d come running and I’d throw some treats into the pen and he’d go get them. Then I was able to close the pen up with him inside.
Eddie was the easy one for this. Lolli was a bit smarter and she knew what was up, so she’d snatch a treat, then run out before I was able to close the pen. I learned to allow for an extra 10 minutes to try getting her back in there. It usually didn’t take that long and on the rare occasion, it took longer, but sometimes we “stoopid hoomins” have to adjust OUR behaviors for THEM. It’s just easier that way. LOL