IBooks
After update iOS 9.02 my files do not get uploaded into iBooks- on my iPad. Please solve this problem- thanks.
I have the same issue, however what I have found is that iTunes keeps switching from "All Books" to "Selected Books" - and of course new ones you've added aren't yet selected.
I just witnessed it switch between these settings in front of my eyes while I was mid-sync.
If you switch back to All Books, it should transfer them again.
BUT it's not putting them into the preassigned categories any more. This latter has always been an issue for me on my iPad, but now it's an issue on my iPhone as well. You can manually move them into the category you want though.
Anyway:
1. Ensure "Sync: All Books" is selected
2. Look in All and scroll right down, it seems to sort alphabetically whereas My Books used to sort by date
If it's still not there, you can open it from the iCloud drive on your iPhone/iPad (if you have the book in a folder on there) then "Open in iBooks". Which is an absolutely ridiculous workaround, but at least it will get your book into iBooks.
I saw devs having problems with this in the developer beta forum, so hopefully it's a known bug they'll fix.