The method you use is the one I use. Once the liberates ebook is in my Calibre, I move my purchases to my Kobo archives, so that the only copy on my devices will be the de-drm'd epub. I normally do that before transferring them to my devices. I bought 9 books from Kobo yesterday, the whole prcocess, including updating the metadata on the 'freed' content, only took about 15 minutes all up.
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