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That's very strange, I've never had a problem using Calibre to download books to my Kobo. When I look at Kobo through Windows Explorer, each author of a book I've downloaded from Calibre has their own directory, and there is an .epub file of every book I've downloaded.
I wonder if you just created the author directory on you Kobo, then copied over the .epub file from your computer, if Calibre would recognize it.
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