Is she having trouble climbing into the box at all? Maybe her abdomen was still sore and she bumped it on the side of the box climbing in and that discouraged her from wanting to use it again? That's the only thing I can think of as far as the litter box. Retraining her to use it was a good idea though so don't give up!
Maybe she's like my guy who suddenly decided to change his potty habits. For no apparent reason he started climbing down from his wheel to use his litter box when he needs to go. Maybe he thinks he can avoid footbaths or something but he will not poo or pee on his wheel anymore. Not that I'm complaining, of course. It's just odd. Hedgies are such weirdos!