For some reason when Apple unhinged Ibooks from Itunes it put all of my PDF’s in an Unknown folder under Music in Itunes where I could not find it. Here is where I found them although since I store and backup to an external drive your file structure might look a bit different.
Music/Itunes/Itunes Media/Music/Unknown Artist/Unknown Album
That is it. They were all right there! Nothing else I tried led me to a solution and I searched through everything.
Hope this Helps someone out.
Paul Chase Jr