I had the same problem with anthologies containing time skipping stories with Kelley Armstrong. I used sigil and split the anthology into the separate books putting them into their correct series order and listing the name of the anthology as a tag.
I've done this with many anthologies that had parts from various series in them. It does add more steps as far as chopping the book to pieces, reimporting, manually editing the metadata and such but I only have to deal with 1 author column and 2 series columns (1 for the main series and 1 for combining multiple series that are the same universe).
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