I never use the book numbering feature in Calibre at all. I just modify the title to include the book order. For example, I have all the JD Robb 'in Death' books so after I download the metadata and get the cover in there, I change the book title to, for example: "In Death #01: Naked in Death." And the book displays in Calibre with that title. I can sort by author or title and view the whole series in order.
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