I actually ended up going back and doing some research because I'm really bad at not overthinking these things, and came to the conclusion that the most likely diagnosis was a ependymoma — a nonaggressive primary tumor, and the most common glioma among young children — in the brainstem/upper spinal cord. Ependymomas don't really respond to chemotherapy, so she wouldn't lose her hair that way, and the position would let the surgeons go in from the back; she might have a bald spot low in back, but one that's easily covered.
(Nico probably was having offstage headaches, vision problems, incontinence, and seizures; staying all Nico-Nico-Ni through it is impressive.)
The couple of months of post-surgical retrograde amnesia would then be a result not of the surgery itself, but sort of due to the brain's rebound after the cranial pressure was released; probably the whole period while she had the tumor is fuzzy at best.