Normal types of protrusions through the roof such as skylights and chimneys do not pose a problem for metal roofs. They need to be flashed and detailed properly and quality metal roofing manufacturers will have instructions to help installers with that. Skylights must be curbed, not flush-mounted with any metal roof. If there are existing skylights that show deterioration or if the existing skylights are 10 or more years old, we suggest new skylights be installed. Even the best skylights have only 20 year warranties. It does not make sense to install a long term roof with a skylight that will soon need to be replaced. However, yes, you can enjoy your skylights with a beautiful metal roof.