A.If the stains are rust trails, they could be coming either from the cut edges of the roofing or from the nails. More than likely it is from the nails, so use stainless-steel nails or screws to secure the flashing.
If the stains are dark, the corrosion is probably caused by a galvanic reaction between the skylight flashing and steel roofing panels. Some skylights come with pre-formed copper flashings that will react with the cut edges of the steel roofing panels in a relatively short amount of time. The stain could also be coming from a reaction between...
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