I had the same issue, although not the same quantity.
Currently the Evernote Knowledge-base says that it is not possible to automatically find and remove duplicates. Their suggestion is:
... follow these steps to manually remove many of your duplicate notes:
- In your Evernote client application on Windows or OS X, change the view to List View.
- Click All Notes.
- Sort the notes alphabetically by title by clicking the Title heading above the note list.
From here, you can look at the note titles and identify and remove duplicate notes with relative ease.
Taken from https://evernote.com/contact/support/kb/#!/article/23193597 (Dec 2014)
Which is what I did, but I can imagine this is not a great option if you have a large number of duplicates. (Relative ease being a subjective phrase.)