Since last update of ibooks most of my books have gone!

You should be able to re-download them for free (as long as they are still available and you use the same iTunes acocunt that you bought them with) by tapping the Store button and then the Purchased tab : re-downloading

Redownloading alone won't work for me because I store some of my own PDFs in iBooks. So I'm now restoring the iPhone to factory settings and will then restore all my documents. I have plenty of time to make this response because this process has about 20 minutes to go. This seems like a big glitch.

PDFs in the iBooks app aren't included in a backup, neither iTunes nor iCloud, you will have to re sync them from your computer's iTunes