I have had continual problems with transferring books to the KT using calibre - so now I no longer use the "send to device" calibre command. Instead I use the calibre content server. All my books are set up on the content servers. Then I download them wirelessly to the kobo using the browser. It's a bit clumsy but they always show up in the memory - which they weren't doing before.
Another way is to drag and drop the epub file - and put it in the top directory of the kobo - calibre seems to create a folder per author, I don't use these. Drag and drop seems to work as well - and I haven't had problems with the metadata.
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