Crashnburn, I have no direct solution for your concern, but some excellent advice for you:
Just stay away from iBooks if you're serious about reading e-books or PDF files. iBooks is simply mediocre software for reading EPUB books, and mediocre software for reading
and especially annotating PDF files. In fact, I find iBooks not just mediocre, but unusable for me (for serious use).
Do yourself a favour and invest a few bucks to buy the best PDF app for iOS, which is
GoodReader. It's
superb especially for annotation purposes.
I also like and use
PDF Expert -- it
looks much nicer and more polished than GoodReader, seems faster, and offers a true Night Mode. However, the
iPhone version of PDF Expert is completely inferior, which is the main thing that prevents me from switching from GoodReader to PDF Expert, because just like you, I need reliable syncing and backup of annotations, which is exactly what GoodReader does so well.
