I have a book I’m reading that I received from a book publisher. It’s an ePub file, which works well with iBooks. Since I love the interface in iBooks, I loaded the file on my iPad 3 and my iPad mini, so I would have it at home on the larger iPad and on the go on the smaller one. Sounds great, right?
I’d hoped to be able to sync my bookmarks, though, so I could bookmark the novel on one device and then pull up the bookmark on the next device I was reading it on. I couldn’t. I spent some time messing about on the internet, trying to figure out how to fix this issue. Apple has the answer, and it’s a lot simpler than I thought.
If you’re having issues syncing textbook or ePub annotations or bookmarks between iOS devices using the iBooks app, you need to update all your iOS devices to the latest version of iBooks, which is 3.0.2 at the time I’m writing this.
First up, tap into the Settings app, then scroll down the left column to the iBooks settings icon. Tap there, and make sure that Sync Bookmarks is set to ON.
Then, launch the App Store on each iOS device.
Make sure you’re logged into your iTunes account, first of course, which can be done under the Featured tab: scroll to the bottom and tap the Sign In button. Enter your iTunes credentials, and then the App Store will know which apps on your device need to be updated.
Now tap the Updates tab at the bottom right of the screen, and scroll to where you see the iBooks icon. Tap Update and wait for the new version to download.
Source: Apple Support