We have a new ordinance in town that should make the process for securing a zoning permit more cost-efficient. It reads: if any application [...] is denied by the Zoning Officer, the Applicant and Zoning Officer are to confer and discuss the basis of the denial. If the Applicant amends or corrects any application for the same permit being sought, such re-submission to the Zoning Officer shall not result in the payment of another application fee.
The idea here is to foster dialogue and cooperation between residents and the Zoning Office. So give it a try, get your permit applications in, and pursue opportunities to improve your home or property.