My idea was it was autoimmune hemolytic anemia at first. It's commonly found in children, and in her age group the treatment would be immunosuppression. Then it seems to progress to Guillain-Barre syndrome, which progresses rapidly as shown in the anime. Furthermore, it seems she didn't lose sensation in her legs and also to be mostly affecting motor neurons in her case. This is often caused by immunosupressive treatment or infections (so it may be true even if she has a different bone marrow disease, as the risk for infections would be higher). What doesn't fit the story to me is that it could be easily recognizable in the hospital and quickly treated without surgery. But I guess doctors can make mistakes?
Also, could someone point me to a discussion regarding what the mother had? (I was thinking antitrypsin deficiency for that one)