This style seal is known to leak, hold water, then RUST!! (ESPECIALLY ON VANAGONS) This is the correct way to stop rust. You have to blast it all out of there and get every bit of it out!! I also like to go even further using phosphoric acid to make sure I got ALL the rust out, incase there was any hiding between the sheetmetal. I used ZINC RICH primer as another rust fighter, it was what I used on the bare metal. Zinc acts as a sacrificial anode and will slow the rusting process down if it were to ever start again. I siliconed the seal too. I did everything I could to stop this. Now I can install my new panel, the window will be completely sealed, and won't drip water all over it!! No rust either!!

This is a good read, its where I got the silicone idea from.
https://www.thesamba.com/vw/forum/vie...

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