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My approach was maybe a tad convoluted (like many of my solutions).
I added a custom text column "#subseries" with heading "Sub Series"
I added a custom column built from other columns "#subshelf" with heading "Subseries Shelf" and formula "{#subseries:'test($,strcat(field('series'),' - ',$),'')'}"
Then in the Kobo driver configuration I had both "series" and "#subseries" listed in the "collections column".
This allowed books from Discworld to end up in either just "Discworld", or both "Discworld" and "Discworld - Witches" and kept the series number as being the series value within the main series.
I realize that this won't help those with two distinct real series but intersecting books.
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