Roof Putty

It was originally filled with lead. If it's not crumbling and falling out, leave it alone. If you need to replace it then a product like All-Metal (a filler) works great. It can be topped with standard body fillers to finish.

In your case you'll want to remove the putty someone applied and deal with the rust properly. Surface rust can be removed but cancerous metal (holes) needs to be cut out and patched or replaced.