Whenever a person receives a new or revised permit after a stop work order has been issued for a site pursuant to Section 14A-3-306 or after work has been completed at a site either without a required permit or not in conformity with the terms of the permit, the subsequent permit must cover all previously-unauthorized work at the site. The building official must add a penalty to the regular permit fee provided in Section 14A-4-412.1 or 14A-4-412.2 for the subsequent permit as specified in Section 14A-12-1204.4.