As MastiffMike said, you can enter the book twice, and then edit the "series" field to show a different series for each copy. I just finished doing this for some Harry Bosch books that cross over to Renee Ballard series, so one copy might say "Harry Bosch [21]" while the other says "Renee Ballard [3]" Calibre will warn you that you are adding a book already in the library, but it will still allow the duplicate entry to proceed.
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