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I am also considering this problem and is trying to write some scripts to fetch the notes from the reader.
The problem of exporting the notes is not so difficult. One has to dig a litter bit in the cached xml files, but I think it is doable. The freehand writing is just common svg file which should be easy to handle with something like inkscape.
The difficulty might be to include all the notes again to the original ebook file, address the position of the note.
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