One possibility that comes to mind is that you are attempting to copy Kobo Plus ebooks from the Desktop app to calibre. That does not work. OTOH, if you download the books to your Kobo reader and then use Obok to copy them to your calibre library, that does seem to work.
Otherwise, what version of the DeDRM package are you using? You should be using the v10 version from NoDRM's GitHub.
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