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I have a small fixed skylight and figure that during winter it's no problem to block the tunnel at ceiling level as suggested by an answer to a similar diy.stackechange question. (The only difference is that I like the light the skylight provides, so rather than rigid foam I am thinking of using clear multiwall polycarbonate panels that provide an R factor of 2 or more.)

The skylight is over a stairwell and difficult to get to so I'm thinking about leaving it in place year round. What would happen if I were to leave this in place during the warm months? It's dry and hot here in central CA in the summer, but would I still be at risk for condensation or mold on the drywall tunnel?

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If you do find condensation then you have a more significant problem that you would want to repair. Here's why: The drywall tunnel, being exposed to sunlight should always be hotter than your house, which means that relative humidity will be lower than in your house even if infiltrated with air from your house. That also means that any condensation would only be against the insulation barrier at the bottom. Unless you have other moisture infiltration into the tunnel that shouldn't happen. If it does then you need to insulate the tunnel from inside the attic or else find the leak that's letting moisture into the tunnel.

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...except that at night, the now-insulated skylight will be cooler than the inside of the house, and may well develop condensation issues... especially on the upper skylight surface (which will be the coolest surface, exposed to outdoor air). – TDHofstetter Aug 29 '14 at 14:35
If the interior absolute humidity is that high then I would expect condensation problems elsewhere - e.g., against crawl spaces and other interior windows. At that point the house just needs dehumidification. – feetwet Aug 29 '14 at 15:09

I don't see a reason to block the skylight at all, especially if you like the light. We have a fixed skylight in our house, and I don't recall ever seeing condensation form in or around it. If it does, it may be installed poorly. I would leave it and see how it does throughout the whole year.

We did install a shade in ours, but we rarely role it out.

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