I have also "lost" many collections in iBooks upon updating the iOs. The place they once were is blank and clicking on the blank space has no effect. I also can no longer add new collections, or they become empty/blank collections, I can't tell.
IPad mini won't sync, yet somehow a whole genre of music and all its files have disappeared from iTunes an this device.
Three of the five functions I most need have not worked at all since the update. ITunes deleting audio-files I need for class, iBooks hiding collections and thereby becoming useless by denying access to pdfs I use for class and no new podcasts because I can't sync.
How does one contact Apple directly to fix these problems?