Typically, after upgrading a Supervisor, you convert JACE controllers to N4.0—or at least you convert all those for which you successfully migrated a station. During the N4 commissioning of each JACE, you install this station as one of the steps in the Commissioning Wizard.
CAUTION: You must migrate the AX station from the JACE and confirm that the migration was successful first (all Programs report {ok}, for example), before installing the .dist file.