It would appear if I identify the nodes, I can modify the 'qname_ns_id' reference in alf_child_assoc from the 'empty' id to the correct id, then this should resolve the issue. I just need to validate that data integrity it maintained.
I appreciate the information on the import tool and I will look at this for future projects. Its just not feasible to re-ingest all the data as it would not be completed by now.