Hello willcodeforfoo,
If the chunk is already georeferenced, you can right-click on the base map in the Ortho view and choose Add Marker option - new marker instance will be created with the 3D coordinates assigned. Then you need to adjust that marker's projections manually on the source images.
To use the coordinates of such markers for the model georeferencing, check on them in the Reference pane and press Update button on the pane's toolbar.
Note that DEM and Orthomosaic need to be rebuilt, if they have been generated before updating the reference information.