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However, there are situations where you can't do that as the manufacturer did not anticipate the material you want to use. In that case, we use some basic principles to guide us (we have installed many metal roofs, with or without skylights). Remove the outside part of the skylight and waterproof the internal frame with membrane or similar material. Provide an exit path for any water that the membrane may catch. Flash the internal frame with an appropriate flashing (we use what we call the end-wall flashing), so that it holds the metal roofing material in a water-proof channel. Make sure the water channel has an appropriate exit (otherwise the water goes into the roof). Caulk the joints (metal to metal joints can leak), and replace the outside cover of the skylight.
In situations where we cannot get the manufacturer's recommended kit, we end up field-forming the flashings to allow a custom fit to the situation at hand. In some cases, we've had to reinstall the skylight assembly itself as the original installation was not properly done. We usually ask the field rep of the skylight manufacturer to verify our work (to preserve the warranty), and so far we've had no problems.