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I noticed a leak on mine a while back and also the sliding window section when closed had a bit of play and didn't seem to be compressing the rubber seal. Traced it back to the plastic ends of the locking rods (2 long metal rods in the picture above) being broken. These pins locate in the holes of the frame. The end of mine was missing so it was a loose fit in the frame.
You can get either from VW (£?) or aftermarket (£8ish) a replacement latch kit with all of the above. In my case all I used was the long metal rods. Above is for a T5, I think the T6 has a different looking latch but maybe the internals are the same.
Tip when fitting is to have the side door closed, you have to compress the spring and locate it on a retaining clip (the 2 small sections top right of the picture). One of these pinged out while I was fitting and ended up under a hedge. The replacements in the kit didnt fit as well as the VW originals. (and im not that impressed with the VW ones either).
Quick edit: the cover pieces are removed starting at the end furthest away from the latch. i.e by the frame.