Duct work is rusting and will be a problem.  We are recommending cutting the entire above roof duct structure.  This could certainly be a reason for it to leak currently in coding or prevent this from happening. The joints need to be coated well to prevent leaking.

The roof service needs to be cleaned and prepped before coating.  Once the surface has been cleaned it is OK to apply a rust inhibiting primer and a topcoat to prevent any leaks.