I quit putting my PDF into iBooks because, last I tried, iBooks would not back them up and the only way to get them out is to email them to yourself.
Now, if you bought any books from apple, you can redownload those. But I quit buying books from apple because you can only read them on an idevice. If you buy from amazon, you can read your stuff just about on any device. I love my iPads, but I don't love being locked in.