As a a couple of others say, use drag and drop instead.
I use calibre as well - it worked fine until I used it to delete books from the device. Now whenever I use the calibre "send to device" command, the books never show up. Now I use Windows explorer to drag the epub from my calibre library folder to the top level directory on the kobo (rather than the author folder directories).
Works for me - but I would like to know why it doesn't work using standard calibre functionality. Never got to the bottom of that one despite asking in the calibre forum
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