IPad to iPad2 PDF Transfer

I am trying to move from my iPad to a new iPad2. I backued up my iPad on iTunes, and restored from that backup and I am having trouble geting my PDFs in iBook to transfer. Everything else seems to work. Any ideas?

What app are they in ? If iBooks then you can connect the iPad 2 to your computer's iTunes and do File > Devices > Transfer Purchases (that should copy PDFs and/or epubs that are in the iBooks app, not just actual ibooks) to copy them over to your computer's iTunes library - if you are using a Mac with OS X Mavericks on it then after doing that open iBooks on your Mac and do File > Move Books From iTunes. You can then sync them to your Air

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