FWIW, what I do is just make a copy of the calibre entry (i.e. the same book is listed twice) but each with a different series. Sure, it means I'm wasting a little storage space, but I'd rather that than the alternatives.
It also helps that I only do this when SOME books from one series fall within another series. However, if an entire series can be considered part of a larger series, than I just go that route.
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