Either he is using his Genjitsu on her right now, or Tobi/Madara has the ability to regenerate or take on new body parts. NO way they leave him as is. (with a missing arm) Or it could even be that he will use or say he taught Orichimaru how to use the body take over technique and simply move to a new body. There are so many ways he is fully healed next time we see him after the battle.