I'm not sure but I think it's Brad Kern who keeps the Book of Shadows, and about Shannen's leaving, maybe the WB wanted to keep the suspense about who was gonna die : Prue and Piper were dying because of their injuries made by Shax and Phoebe was supposed to be killed by one of the Source's henchmen. If Alyssa were the leaving one, I think the 4x01 episode would have been approximately the same, with Prue surviving instead of Phoebe.
P.S : Are there any spelling mistakes ? It will help me to know about that.