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Sounds like the Kobo desktop and/or ADE could be the culprit.
It is worth trying out Calibre. It will see your connected Kobo and allow you to transfer files accross, either DRM'ed ePUB or non DRM'ed ebooks that Calibre will convert to ePUB if necessary.
One thing I have noticed though. If your ebook is a PDF, Calibre will not convert to ePUB and send that ebook to the Kobo. It will send the PDF directly. Best to convert to ePUB before transferring the ebook to ensure the ePUB is the one transferred.
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