About the flashback, this is what I have been thinking for about ten chapters. I think there is still the possibility that Kiruko's brain is still only the brain of the older sister. It could be a severe act of self-conviction (as in another famous manga by that I don't want to spoil) maybe due to mourning or guilt for the loss of the little brother. Stopping menstruation can be caused by this, even the scar on the head is a proof that she was operated but not the brains swapping, the memories instead can be a construct of the psyche, maybe the little brother never even existed.