Did you have any pdf's in iBooks? If so did iOS 9 wipe them out? (Did to mine). If so, did you find a way to get them back?
*Wiped all from my iPhone 6, wiped none from my el capitan Mac, wiped all but one from my iOS 8.4 iPad air 2. (I begin to wonder if by not going to iOS 9 public beta on my iPad has blocked iBooks from syncing all the pdf's back from the Mac.)
I use notability a lot more these days than iBooks because you take notes and highlight better. So I had not tested iBooks yet. I just went into my iPad and iPhone and the key PDFs I was expecting to find are still there, so it does not seem to be affecting me (iPad Air2 and iPhone 6). The health app, on the other hand, crashes all the time.