Hello JHP,
If the details of the scene looks more or less similar on both sub-sets and therefore the tie points can be detected between the photos from different sub-sets, you can try to uncheck all cameras in the Reference pane and run the Align Photos operation with Reference pre-selection disabled, using only Generic preselection.
If the sub-sets are adequately aligned with each other, you can check on the coordinate data in the Reference pane and optimize the alignment or just press Update button to georeference the result.