The rust is from the reinforcement in the rubber,
the rust molecules migrate through the painted surface, meet with the aluminium & cause a BI metalic reaction.
get the seal off and a new one fitted ASAP , the dealer will replace it with a new seal.
if it were me I would pull the seal away gently, photograph it, clean the area thoroughly, repair any damaged paintwork (primer, touch up paint & clear coat)
if no repair necessary simply apply some easily removable tape, such as sellotape to the affected area ASAP to block any further rust contamination of the paintwork whilst awaiting the new seal (remove tape before it goes in for the new seal)
if the rust has contaminated the paint, fall out remove may remove the staining from the rust.
if left this will develop into bubbling paint and roof corrosion.
i a, on my fourth roof seal since 2018 (new van)
i Check the seal every six months, dry, clean and apply polish to the entire edge of the roof.
VW are fully aware of the dire situation since the T5 and have chosen to do nothing to prevent the issue from occurrin.
there is a VW dealer wide work shop action which requires dealers to replace faulty seals whilst under warranty.
All dealer should be aware of it.
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