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The previous owners installed a metal roof over existing shingles less then 10 years ago so we were told the roof should last at least 20 more years. A heavy rain revealed a leak from our skylight. Once on the roof it became obviously that the metal roof was installed over the skylight and caulked off. No proper flanging was done (see pictures). The ceiling with the leak is showing significant mold damage and likely encompasses a much larger area from the leak going on so long. We know how to replace the ceiling, but the roof is another matter. The skylight probably needs to be either replaced or removed entirely, but we aren’t sure if mold has also damaged the shingled portion of the roof. Since there is mold, we are hesitant to start poking around until we are ready to make repairs. At this point would it be better to remove the skylight or is that not an option because the metal roof is resting on infrastructure of the shingles roof? Can we even replace a skylight on a roof like this? enter image description here

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  • Keep in mind that if the skylight is deleted, the "patch" of new roofing will be rather obvious. Even the same brand and same color code will look different because the existing steel has faded somewhat over 10 years and the new stuff won't have faded at all. If you're really picky and it bothers you, you may be in for a replacement of the whole roof to make the color match. That's totally your decision, though - just something to consider before deciding to scrap the skylight.
    – FreeMan
    Commented Sep 23, 2022 at 11:47

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I am surprised this was not caught by the home inspection company when you purchased the home. And, if you did have an inspection there might be some liability on their part that could recover some of your repair costs.

Choices are to either remove roofing and install the skylite properly with correct flashings etc. And yes, this can be done properly. Another option is to remove the skylight and roofing around it and inspect/ and repair any damage to structure then close the hole and add roofing to cover where the skylite was. You will also need to repair/ match the ceiling finish inside. Either of these options are pretty extensive and probably not DIY projects.

The only other (short term) option is more/ better caulking.

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  • It's rare, but I'll agree that this may be a good time to call in a pro for this work. Skylights are notorious for leaking when not installed properly, plus the added "fun" of working with steel roofing. The good news is that unlike shingles, I'm betting that the steel can simply be unscrewed, then after replacement/repair of the skylight, most if not all can be screwed right back down without any new material being needed.
    – FreeMan
    Commented Sep 23, 2022 at 11:45
  • TBH, though, I'm not at all surprised that this wasn't caught by the pre-sale home inspection. My inspector looked at the roof (2 story farm house) from the ground, and had me look inside the attic because the attic access is tiny (I barely fit at the time) and the inspector, umm, wasn't tiny.
    – FreeMan
    Commented Sep 23, 2022 at 11:49
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A heavy rain revealed a leak from our skylight.

Yeah, that's just a universal problem with skylights. They are very hard to seal, and the seals need a lot of maintenance, and they never get it. Of course by the time the leak is bad enough to notice, the damage is done.

At this point would it be better to remove the skylight or is that not an option because the metal roof is resting on infrastructure of the shingles roof?

Well I'm no fan of skylights, so I'm biased toward removing it. You would need to fill the hole with framing and OSB/plywood so that it is level with the framing and OSB of the rest of the roof. (so that when you finally remove those shingles, the OSB on the patch is level with the adjacent OSB; or if the OSB is rotted and needs to go, the framing on the patch is level with the original framing so the new OSB can go down without drama.)

The choice to lay it over the old bed of shingles is unfortunate. For the patch, you will need to come up with a spacer the same thickness as the old shingles, that is also removable for when the shingles go away. But that could be a long time. Metal roofs last a really long time.

But the trick will be finding the same exact stamping of metal roof so that the new sheets just key right in. Then only the 2 sheets need to be replaced.

Color match will be a problem, so painting the roof will be necessary if you don't like the stripe. Follow manufacturer advice for painting. By the way, if you like to save money on air conditioning and have a cooler attic, white is fantastic.

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