Transferring PDFs from iBooks to your laptop/desktop There are a lot of tutorials on how to load PDFs into iBooks, but none say how to backup or transfer them back to your computer. I understand there is a button to email them, but I probably have accumulated 100 or so useful pdfs on my iPhone. 

I worry if I click sync books, it will erase everything I have on my iPhone and only use what's on my computer the first time I do it right? I have never synced it before loading the books.

Is there any safe reliable (hopefully native) way to preserve books and PDF that were loaded natively from iOS? I do not want to risk losing them. I'm using iCloud, does that back them up as well? Either way I would like to have an extra copy of them on my hard drive.
Grab a copy of iExplorer (freeware), connect your phone, open iExplorer, select your device, and navigate to Media > Books. All your PDFs should be there.
However they all have cryptic names and there's no QuickLook in iExplorer, so you need to copy them all and then look which ones you need.