His question startled her for a brief moment but then she realized what he meant. He must have been feeling some sort of aftershock, his brain unable to process the idea that nothing was physically wrong with him anymore. She remembered a few months ago when she had died herself, and how the place she had been shot had been painful for a few long hours after the incident. She knew there was no wound but her body didn't, and that was the main problem.
Knowing there wasn't really any cure her jutsu could be useful for, she nodded anyway. If his pain was going to go away Sakura had to make him think she was actually able to help. The pain was obviously all in his head, not that it was his fault. "I can do my best," she said with assurance. "Just show me where and if it doesn't work right away, don't worry. You'll have to stop thinking about it by doing something else. Maybe if you talked or... something."
She hoped getting him to talk while she attempted to work would have some sort of effect.