Why are the empty fields there to begin with? Can you start without the empty fields and just use the two columns produced in the join? I think this is the simplest approach. Either that or find a tool similar to the "Load" tool in ArcGIS.

https://desktop.arcgis.com/en/arcmap/latest/extensions/production-mapping/loading-data-into-a-geodatabase.htm

Are you using a geodatabase? I highly recommend this.

Why are the empty fields there to begin with? Can you start without the empty fields and just use the two columns produced in the join? I think this is the simplest approach. Either that or find a tool similar to the "Load" tool in ArcGIS.

https://desktop.arcgis.com/en/arcmap/latest/extensions/production-mapping/loading-data-into-a-geodatabase.htm

If you are not using a geodatabase, I highly recommend this.