Thanks BetterRed, that worked!
In my case, the ZIP file contained copy of the PDF book. This is in case the book gets modified (through annotation, etc), and I then need a virgin copy.
Based on my understanding of the Archive Extract plugin, I suppose the expected behavior would have been the same as when the user tries to associate a new PDF with a book record that is already associated with a PDF (a warning like "this will replace the existing PDF").
Would it be appropriate to file a bug report on this?
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