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Interesting. Is there technically a primary and secondary series recognized for these books in print.
Using common epub2 meta metadata tags with just name and content attributes are then an issue as there is no explicit relationship between a calibre:series_index meta tag and the calibre:series meta tag if there exist multiple series. With only meta name and content tags to work with you would need to create a calibre:series2 and calibre:series2_index just to prevent mismatch between index values and series titles. Obviously, this does not scale.
Alternatively, fixing the exact sequence of meta tags in the ops metadata section is the only other approach that may be usable where the series_index meta tag would have to always come immediately after the series meta tag if multiple series tags exist. But there is no easy way to enforce that.
In epub3, the use of refines with target ids actually helps here.
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