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I think your issues are because something is corrupted. I would delete the books.db file to force it to rebuild the database or else reformat. I was syncing hundreds of books. The only duplicates of notes that I had were because I had two copies of the same book (one on the main memory and one on SD). Have you looked at the files on your T1 in the Finder window? Do you maybe have multiple copies of the book on your T1? There is a box on the sync screen related to highlights and notes. Do you have that checked on?
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