Thermos

I've got rust bubbles forming just above the windshield and I intend to (try) and take care of it myself. I don't care for the result to look spectacular. I really just want to eliminate the rust. My approach is to scrape the bubbles off, sand the affected areas, apply a rust converter, and paint on top.

The problem is that some of the rust is below the rubber strip and I wonder if that's something I can pull out and then place back in, or is it a part that requires some kind of glue to be (re)installed properly? Can I even re-use the same piece of rubber or will I need to get a new one?