Yeah it was pretty obvious from the beginning that the sister was dead. Backstory from last chapter provided additional background: she had to go to the nurse's office every day for the previous year, but now she is suddenly normal. She was likely terminally ill with something and receiving maintenance treatment from the nurse each day. She died in the summer which is why no students noticed the gap.
Only weird part is why the dad was such a scumbag and didn't inform either Sayuri or his ex-wife about either the illness or the death. Based on the fact that she can still go the same school, I'm guessing she actually lived close by the whole time, no more than half an hour away. Not informing very close family members who live practically in walking distance of a dying family member is so fucking cruel it should be a crime.
Amusing side note: it was only out of chance that Sayuri didn't call her father at the beginning. I guess she will eventually and then learn the truth. Either that or they'll finally have sex and she'll disappear because her wish was fulfilled.