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Without knowing the specifics of the skylight brand and condition, we would not be able to answer the question with confidence.
We use Velux skylights. During re-roofs, we typically find most skylights are not in good condition and/or were not installed properly.
Probably need to have the skylight reflashed. Skylights need to have special flashing kits designed for skylights. Have a professional come to inspect to see if you have a curb mount or deck mount skylight and they will be able to give you a price to replace your current flashing with a new airtight skylight flashing kit.
First make sure there is weather stripping between the skylight frame and the curb, assuming this is a curb mount. sometimes there is not a seal inserted at that joint. If that is not an issue, then you could certainly install a frame around the well at the ceiling level and insert a piece of clear acrylic to keep cold from dropping into the room. I have done this at a previous residence with great success. Good luck
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