Syncing iPad with iTunes removes PDFs from iPad

Question

Hi, this is only a small annoyance, but I'm hoping someone has a clever way to save me a few steps that I have to do every time I sync my iPad.
As a student, I use my iPad to download PDFs quite a lot, and I move them into "collections" to keep them sorted under the relevant subject. This all works fine until I sync my iPad. Then, because I have chosen to sync "selected books" instead of "all books" (there are way too many PDFs on my hard drive) all my new PDFs disappear from the iBooks app on the iPad, and they can't be located by name when using the "Search iPad" function either.
My workaround is fairly simple, I go to the "Books" tab for the iPad within iTunes, sort the books by date instead of title, and check all of the new PDFs that I still want to keep on the device. Then I sync again, and presto! They are back. Still, it seems a little silly that if I actually download the PDF on the device, there isn't an easier way to make these PDFs behave the same way that, after all, purchased music does on the iPad - it assumes by default that you will keep those songs synced, and you have to take steps to remove them.
Any thoughts? Is there some way to make a "smart playlist" of books & PDFs that are newly added, so that my old hordes of PDFs are kept off the iPad, while new ones are by default present, thus avoiding the risk that I forget to re-add them after syncing and find that they have disappeared?
Thanks o wise ones!

Answer 1

Hi Www2013,
iTunes will not back up automatically if you are using iCloud.
iOS: How to back up
http://support.apple.com/kb/ht1766
This is the data that iCloud backs up.
iCloud: Backup and restore overview
http://support.apple.com/kb/HT4859
Backups do not contain content synced to the device, such as movies, music, podcasts, and apps.
iTunes will back up the following information
iTunes: About iOS backups
http://support.apple.com/kb/HT4946
Hope this helps,
Mario