I was thinking that maybe a thin rubber strip sandwiched between the body panel and runner might be a better idea? I suspect that the runner flexes or moves imperceptibly every time the door is opened and closed, and either the movement has rubbed through the paint finish over time or dirt and grit that has fallen or washed down behind the runner acts like sandpaper. Whilst sikaflex would stop muck dropping down behind the strip, it won't do much to prevent the strip and body panel rubbing against each other. A length of rubber the same length and width as the runner would solve both problems.
Something has abraded its way through the outer surface of the panel, since I understand that they're galvanised, so shouldn't rust unless the galvanic coating had also been worn through. I'm thinking of taking mine off and doing it as a preventative measure now!
