I am not sure what is the emotional state of your sub, but you might have a problem on your hands that needs to be resolved with professional help ASAP. There are many people who would say that physical pain is easier to handle then emotional pain, that is why sometimes when someone goes through trauma or just is very unhappy, so unhappy that it hurts them on the inside, it's like their soul is in pain.

In those situations many would start harming themselves not with the idea to harm, but to feel that physical pain, because then the person can concentrate on the physical pain rather then on the emotional.

As I said I do not know what your sub feel or thinks, but if the case is similar to this, it can be very dangerous since in a vanilla relationship such a problem can be easily noticed and dealt with. But when pain is a part of everyday life, you might not know if she needs it for sexual gratification or to block out her emotional suffering. Please talk to her and ask her why does she need it. If you believe you can handle it then do so and if not then seek professional help. In either case do not ignore it.