This issue has happened to me on the last two updates! I updated about a week ago, and then spent 2 hours fixing all my duplicates. I then saw yesterday that an update was available, and hoping that it had fixed the dupe error, updated again. Now i have 3 copies of the notebooks, with 1 being a syncronised notebook, and the other two being 'local' notebooks. Where did they come from? A real pain, and it happens repeatedly when I downgrade and re-upgrade. So I for one am unsure as to why Evernote is having trouble replicating it internally...?