I'd strongly recommend staying away from the sync feature. It simply isn't worth the pain. I made the same mistake and ended up with a whole bunch of duplicate bookmarks. It is poorly implemented and doesn't really provide any benefit. I'd suggest you look into using Calibre for managing your library and transferring books to your readers. I'm doing that right now, and I love it this way. Calibre is far more robust and useful than the Sony software.
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