If she has a really messy bottom, then it's possible that fly strike will be a concern. Can you have someone hold her, while you clean her?
My big French Lop girl, Cher, is the messiest rabbit...ever!! Her bottom was always a mess. I finally figured out why: her poo balls were too big to fit through the wire on the cage floor, so she'd go and then sit in it. Anyway, I put her on my grooming table (which is a chunk from an old cabinet, with a laminate top). I kept her feet on the carpet piece and then used a water bottle to spray her bottom to get it wet. Let it set awhile, then rub with a paper towel. I also clipped the hair that was messy (mostly at the base of her tail). I just kept doing that, and after 2 days have it almost all cleaned up. There's still staining, so I'm using vinegar/water and cornstarch to try to remove those.
