If all empty books that have been deliberately created have a corresponding folder on disc then a simple routine which compares the database to the disc and produces a report, showing database entries with no corresponding folder on disc which gives the option of updating the database to match the disc might be a very simple way forward.
I say simple, as I assume you would find this a simple routine to write based on your experience, for me it would be like trying to climb Everest :-)
Maybe this could be an additional option within Library Maintenance called 'database to disc check'
Regards
Ian
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