Interestingly, the second page of the banns book has 'Parish of Holywell' written at the top. However, those who actually show as being married Bagillt in themarriag registers, show as St James, Holywell in the NW BMD.
Add - I did some of the transcriptions for the NWales BMD (not Flintshire) and we used the record office (Registrar's ) books. A query to the records office might solve the puzzle.