ibooks
I recently synced my iPad 2 to my PC in order to do a factory reset and update to ios9. I cant find all my books and PDFs in iBooks.
iPad 2
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What exactly did you do when updating ? Prior to starting the update did you do File > Devices > Transfer Purchases to copy them over to your computer's iTunes library (that should have copied PDFs and/or epubs in the iBooks, not just actual ibooks) ? If not then the ibooks that you can redownload will show in the Purchased tab in the iBooks app (and check to see if you've hidden any : Hide and unhide purchases in iTunes or iBooks on your Mac or PC - Apple Support) ; PDFs and/or epubs you will either have to add to your computer's iTunes library (File > Add To Library) and sync them, or download them from wherever you originally got them from