Just as a test, I transferred a few more books from an unrelated 3rd series, and after disconnecting the Libra2 from the PC and letting it do its sync, those show under the new series, and the 2 books that before were orphaned are now also listed under their corresponding series.
Not sure why sending the new books for an unrelated series has sorted the problem, but I'll take it. I can only surmise that adding the new books has triggered a refresh of the database and the 2 new books have updated metadata.
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