How is the health issue going right now for her? In the meantime, ban Lily from the bedroom for the time being so the little one has a box all to herself. Are the sides too high for her to in and out of easily?
When she goes in there, make sure you go in there, too, and when she starts going to the bathroom, pick her up and put her (gently) in the litterbox. If she was never trained in the first place, she might really have no idea.