Roof sealant removal

In the roof or the plastic inner cap (you've got multiple threads on this... :LOL:)? If the roof, I cut a thin aluminum patch a bit larger than the hole, applied poly sealant around the perimeter and stuck it down. Then drilled holes for rivets. I use aluminum rivets with built-in o-rings to seal the holes. I used the same rivets to seal the holes left when I removed the cargo carrier and the roof-rails. Then top with a bit more poly for good measure.

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I filled the gaping holes at the end caps with Sikaflex after removing the remnants of the butyl and put a generous blob of Sika under the end cap when I refitted it. Fixed all tendency to leak.
 
In the roof or the plastic inner cap (you've got multiple threads on this... :LOL:)? If the roof, I cut a thin aluminum patch a bit larger than the hole, applied poly sealant around the perimeter and stuck it down. Then drilled holes for rivets. I use aluminum rivets with built-in o-rings to seal the holes. I used the same rivets to seal the holes left when I removed the cargo carrier and the roof-rails. Then top with a bit more poly for good measure.

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I thought I knew all of the types of pop rivets, that's a new one on me.

The O-ring is interesting but the rivet doesn't have a sealed end. The 3-legged Olympic style pop rivets (aka Bulb-Tite) are wonderful in the right applications, but the gaps between the splayed legs and the open end seems to be counter-productive to the O-ring providing a watertight installation.

The splayed legs of an Olympic type rivet are meant for additional attachment strength (not needed when just sealing a hole) or when the backing material is soft (plastic or rubber).

The additional sealant you put over the heads means you won't have to worry about what I just wrote! 😉