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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?

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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.

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