From the look of it, as I haven't played in a few months, it seems to follow some of the same story, but "Fae" became "Numina", they're no longer hidden from humans, and the personalities of the girls have been altered quite a bit. Emma's no longer the shy, petite singer. She's become an employee of Jessica's hotel, has completely changed her style (I literally didn't recognize her at all), and isn't nearly as shy around the MC.
I might play a bit more to see what else changed since the last time (Four months ago for me as I write this), but I'll be looking for, and re-downloading, the old version's last update, and just enjoy that story for what it was.