The only thing I'm surprised at is that Saki didn't confront her parents about the disappearance of her older sister, especially now that she remembered it. It's not the first time it has come up, her mother is particularly bad at hiding her own distress about her children (though perfectly understandable).
It should be clear by now that what makes Saki special is her unique brain structure, not the strength of her Cantus (which is just below average). For whatever reason, brainwashing simply doesn't stick on her. She recalls details of their collective upbringing/training that the other four don't remember, and now she was unable to unlock the memories of her older sister, something she showed no sign of awareness toward when she first overheard her parents.
I had thought that Saki either wasn't alive at the time her parents had a child (or other children) and that Saki was their "next try" or she wasn't any older than a baby. From the flashback, Saki was certainly old enough to possess self-awareness, and have plenty of vivid memories of her sister. The brainwashing purge is quite powerful to remove her sister's existence so completely. It's even more telling that Saki broke through that.