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Just a note on elminster's technique for restoring notes, if you are ALSO using Calibre. When you reorganize book names, or author names, it changes the directory and filenames, so if you do that after you copy your books back, the filenames and directories would be different, and if you just copy the .annot file to the old location, it won't restore your notes. So here's how the file structure should look (my drive letter for my sony reader main memory is drive H).
If the book has this directory and filename:
H:\database\media\books\Baumeister, Roy F_\Willpower - Roy F. Baumeister_1690.epub
Then the .annot file should be in this directory, with this filename:
H:\Digital Editions\Annotations\database\media\books\Baumeist er, Roy F_\Willpower - Roy F. Baumeister_1690.epub.annot
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