iBooks: Viewing, syncing, saving, and printing PDFs on iPhone, iPad, and iPod touch
Using Sync Collections with PDFs in iBooks
If you turned on Sync Collections, iBooks will keep your PDFs (and non–iBooks Store books) in the same collections across all your iOS devices and Mac (if you're using OS X Mavericks). For example, if you have the same PDF on all your devices, when you move that PDF to your Sci-Fi collection in iBooks on your iPhone, that PDF will appear in your Sci-Fi collection the next time you open iBooks on your iPad.
If you delete a PDF (or non–iBooks Store book) while you have Sync Collections turned on, it only affects the copy on the device. For example, if you delete a copy of the PDF from your iPad, it will still be on your iPhone.
For more information about iBooks and the iBooks Store, see the frequently asked questions and how to sync iTunes Digital Booklets to your iOS device.