Actually, you could manually move the .mbp file (notations) from the iPad to the Mac app by using iTunes on your Mac. Connect the iPad via usb. Select your iPad in iTunes and then Apps. Scroll down to the File Sharing window and your'll see a mbp file for each book. You can "save to" your mack and you now have the notations file.
You could also use a file app like DiskAid
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