It's because what happened in the second part of the first season and the entire second season are not canon. They were retconned when it was decided to continue animating the canon manga arcs starting with Book of Circus. Every adaptation with "Book" in the title is canon as it's based on the manga. (The first half of S1 is only partially canon as, while it adapted the first few manga arcs, it changed a lot for the sake of the plot of the second half which is, like I've said, not canon.)
Undertaker's reveal in the first season was in the second half which falls into the "not canon" Kuroshitsuji material. Book of the Atlantic, however, is canon. It adapted the Luxury Liner Arc of the manga in which Undertaker was canonly revealed to be a Grim Reaper for the first time.