@chris.adams few days ago I created a php file that generated VCARD 2.1 file with the missing contacts:
https://github.com/osnas/sailfish3_contacts_export_php
It seems it worked really well so I will not search further what went wrong any time soon. I checked the git you provided, also tried to run vcardconverter from command line in Sailfish 4, it didn’t work. I suppose it knows where to get the contacts database and there isn’t an option to read specific contacts.db file ?
I will try to find a pattern of what went wrong, if you have any specific ideas let me know.