Nobody has any ideas?????

I have a standing seam metal roof (which I've spent more time on than I like to admit)...it does have skylights but I have no idea how the roofer did them--so I didn't respond. I think he made the flashings out of the same sheet metal as the roof.

Good luck in your search; stay safe up there!

The flashing system you use with skylights depends on which metal roofing system you use. Most (if not all) of the companies manufacturing metal roofing have detailed drawings on this type of detail available for their installers. Some of the skylight manufacturers also have a selection of flashings which are designed to work with specific roofing materials. So probably the simplest choice is for you to contact your skylight installer or the skylight manufacturer and find out from them if they have a flashing accessory kit for your type of metal roofing.

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.

BINGO, pgriz! That is exactly what our roofer told us; the skylights (which were pretty much "home-made" over 20 years ago) were never really properly installed. So the roofer did exactly what you said--rework the entire thing using "field-formed" flashings. (This was DEFINITELY NOT a do-it-yourself project!)