According to Apple, iBooks has an ability to sync bookmarks between iDevices over Wi-Fi. Suppose you are reading a book through iBooks on your iPhone and have some of its bookmarks, highlights and notes, now those will automatically get sync on iPad and iPod Touch as well.
By default, Bookmark syncing is disabled on iDevices, so first you have to turn it ON to make it working, so steps below will help you out to do that.
Sync iBooks Bookmarks to iPhone, iPod Touch and iPad
Step-1
Tap on “Settings” icon on Springboard
Step-2
Scroll down to “iBooks” and tap on it
Step-3
Position the slider towards ON for “Sync bookmarks”
Note: To sync iBooks bookmarks you must have an Apple ID and your iDevice should be connected to Wi-Fi or mobile data service.
See Also:
How to Add PDF Files to iBooks with Dropbox
How to Convert PDF to ePub Format
And when that doesn’t work what do you suggest.?