I've had exactly the same problem. I synced my Kobo Glo yesterday and since then I can't transfer any books from my 'download' or even Calibre, which now says it doesn't recognise the new file changes Kobo has made. I've re downloaded Calibre again and made a small change, and now it says that it's downloaded to the Kobo, but nothing shows up on the device once I've ejected. Don't want to do a factory reset either as all will be lost

- anybody have any ideas?