Maybe she ate the original and decided to replace her after meeting Hinako once and liking her? I don't know, since I don't know what's put in the student register.
I'm actually wondering what was put in the student register to make Shiori realize "Hey, thats not Miko, thats a human eating monster!" Like what could've tipped her off? Her blood type? Doubt its a photo since people could've realized that wasn't her too. I don't know, this is definitely an interesting story so far, but i've yet to see the yuri part of it. Is it vore yuri?