Rabbits don't like being picked up, its scarey for them. Everytime you try to pick her up it's probably making her nervous and upset, and thus she won't trust you as much. Plus your right, if she struggles too much she could hurt herself or scratch you.
If you can, I would find a way to get her back into her cage without picking her up. My suggestions are to either make a ramp going up to her cage and let her get in herself without being picked up, if you can. But since she lives outside that might not be possable.
You can try getting a pet carrier, and when you want to put her away lure her into the carrier with treats. When she goes in, bring the carrier to her cage door and let her go from the carrier into the cage on her own. It may take awhile to get her use to the carrier, put treats in it and leave it out when she's out playing, don't force her into it or make it stressful for her at all because then she won't want to go into the carrier either.
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