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Yes, rickyzhang, I also have that problem... I can't make a backup of notes inserted in pdfs. I can export a pdf with notes incorporated in the file, but it would be much better to be able to backup them directly, without generating a new pdf.
Maybe Booxtor can help us? Information about bookmarks, current pages and notes must be stored somewhere, it would be easy (maybe) to modify user's permissions to access those files...
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