Can't add PDFs to iPad Air without losing ones already there I added some PDFs from iTunes to my iPad and the ones already on it disappeared. When I tried to sync them back, I get the message they weren't transferred because they cannot be found. They are all showing up in the iTunes library now. Now all I have on the iPad are the ones I just added.

There can't be anything wrong with the ones I lost because they worked fine on my iPad before they were lost to it. How can I get the lost PDFs that are in iTunes to sync to my iPad Air?
You don't say how you are trying to sync the PDFs or if you are using Mavericks, so I can't tell if this is helpful or not, but I have been using iBooks to sync PDFs across multiple devices with no problems.

Have a look here

Sync and save PDFs

To add PDFs to your iTunes library on your computer, drag and drop the PDF into your iTunes Book library. If you're using OS X Mavericks or later, drag and drop your PDFs into your iBooks library using iBooks for Mac.