Thank you.
I am facing a small issue regardless the chosen method.
Every time the Libra 2 syncs, it downloads the purchased books from the Kobo Store. I always sideload all my books trough Calibre in order to have them DRM free and with the metadata, collections and all of the information the way I want. Sometimes I even change the cover. So I end up with duplicated books.
I am sure that it is a silly thing that I am missing, but what can I do to avoid that?