Transferring iBooks notations between versions

I just upgraded from an iPhone 3GS to an iPhone 5S, and I had a bunch of files in an older version of iBooks on the old phone that included a number of notes and bookmarks. When I transferred everything between phones, the notations originally transferred just fine because I also originally put that older version of iBooks on my new phone as well. Then I updated iBooks to the newest version and my bookmarks/notes all disappeared. It sounds like that can happen between versions of iBooks, but for obvious reasons I'd like to retrieve my notations instead of having to recreate them. It sounds like I might be able to transfer notations if I update iBooks on my old phone, but I'm concerned if I do that I'll just lose all of them again.

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