Finally figured out how to do this thanks to a gentleman named Heiko at https://discussions.apple.com/thread/5564809 :
- Open iTunes on your Mac and connect your device
- Highlight your iOS device in iTunes
- Pull down the File menu, hit Device, then Transfer Purchases:
|iTunes: Transfer “Purchases” (including PDFs) from iOS device|
All PDFs will be copied to your Mac.
- Now open iBooks on your Mac
- Pull down the File menu, and hit Move Books from iTunes
All your PDFs from iBooks on your iOS device are synced to your iBooks on OS X:
|iBooks: Move Books from iTunes|
Like Heiko, I cannot find any official documentation for doing this. It sure is a lot faster than transferring each PDF individually by email. I don’t understand why this isn’t done during a normal iTunes or iCloud sync.