Thank you for your feedback, @Michael ParisThere was definitely lots of moisture on the floor, but unfortunately the contractor didn't check the moisture level after applying the sealant which we realized now was a mistake.

The top still needs two more coats of sealant, which will make it quite glossy - the colour is "Traditional Oak"The sides I painted with a "Sky Grey" colour. 

The part that concerns me is the shingles with the caulked edge, if there is no step flashing under the caulk, you are almost guaranteed to have problems when the caulk releases, cracks typically within a few month to a few years depending on the sealant used. 

Any penetrations in the will need fire sealant that is UL rated. 

We never charge our tenants for painting to turn a unit ... but in this case I had to use a heavy duty sealant primer to ensure the stains and odors don't come right back up. 

If that's the case a good contractor can replace moldy materials, treat the rest, and apply mold preventative coverings/sealants to the treated area.  

They dig it up, coat it with a sealant, and fill it back in.

Example:https://www.stonecoatcounterto...I had a tenant refinish countertops using two different types of speckled paint, then covering with a sealant.

And always cheap on the sealant and OF COURSE the spray foam (if they even reach for it).

Roofer came back out and looked it over, sealed them with some type of clear water sealant, and said the flashing and everything looked good -- but they continue to leak and the leaks are getting worse with each storm.Question: how do I find the right person to replace these skylights?