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I think if you delete books.db then you will lose your notes. I would probably reformat the memory and wipe everything clean so a sync doesn't accidentally delete notes from your hard-drive copies? Are you positive that all of your notes are in the Reader software associated with the copies on your hard-drive? If so then it shouldn't be a big deal to wipe clean the T1. You can just recopy the books with notes from your computer to your T1 as if it were brand-new out of box. It sounds like you need to clean-up the notes in the Reader software to delete the duplicates first though. Otherwise the problem will persist.
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