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I think the only way to manage that is to make the changes in Calibre that you want on the Kobo. If it's a matter of wanting to add books to a special category, such as your next reads, you're not limited to just one tag in Calibre, you can add as many as you want and the books can be listed in multiple collections on the reader.
But there's no way to stop Calibre from making the changes to only specific books.
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