PDF files on iPad's iBooks won't sync with iPhone's iBooks

I have many downloaded PDF files saved in my iBooks app on my iPad.  They are work documents so nothing that I purchased from the store.  I have everything set to sync in my iBook settings, but when I look in iBooks on my iPhone, only the folders synced, not the actual documents.  Is there a way to get them to sync?

Even though they aren't iTunes purchases you should be able copy them from your iPad to your computer's iTunes via File > Transfer Purchases (File > Devices > Transfer Purchases if you have iTunes 11 on your computer) - you can then sync them to your iPhone.
The sync bookmarks and sync collections settings won't copy items between your devices, it will just keep the the books/PDFs that you have on both devices in-line with each other e.g. if you have a PDF on both and you move it into a collection on one device then it will put into the same collection on the other device.

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