Lost all iBook files after restore. Can I retrieve them?

If they are ibooks from the iBookstore then you might (if they are still in the store and you haven't moved countries since buying them) be able to redownload them via the Purchased tab in the iBooks app.

If they are epubs and/or PDFs from other sources then they are not stored in a backup (nothing in the iBooks, Videos, or Music apps are). An iTunes restore will look for them in your iTunes library (or iBooks app if using a Mac with Mavericks or Yosemite on it), an iCloud restore will redownload what it can from the store. If you have them on your computer then you can sync them back to your iPad.

I am having the similar problem. My pdf files show in the book section but do not appear and will not reload.

If they only appear briefly then they are not on your device (PDFs and other non-iTunes purchases in the iBooks app are not included in a backup), you will have to resync them from your computer or redownload them from where you originally got them from

I find this EXTEMELY annoying. What is a backup if it doesn't actually do the backup. I've lost all my iBooks which were downloaded from other sources as well as those from the Apple store. I have to have a third party program to move everything.

This lack of file control has always been a sore spot with me. I was an Apple basher for years, but fell in love with the iPhone and iPads which I have owned since iPad 1 and iPhone 4s. I have NEVER been able to do a proper backup and restore. Every place I look on the net says how easy it is through iTunes, but the easy answer is that you can always re-download your purchases from the Apple Store or from their original source.

Still love the iPhone, but I dumped my iPad air and bought a Surface Pro. At least when I back it up, it does what I ask it to do.