Why is my skylight leaking when the glass is fine?
Because the waterproofing is in the flashing, not the glazing. The unit is a lid; keeping water out depends on the curb height, the flashing laps and how the roof covering is dressed against it. A failed sealant bead or a short upstand leaks regardless of how good the glass is.
Sealant is the giveaway. Where a bead of mastic is doing the job a flashing should be doing, you have a detail that was never right and has simply reached the end of the caulk's life. Renewing the bead buys a season.
On a near-flat roof the standing water makes it worse. A curb that would be fine on a pitched slope is submerged for a few hours after a cloudburst on a roof falling a quarter inch per foot, and anything below the top of the upstand finds its way in.
Is it condensation rather than a leak?
Quite often, and the two look similar from inside. Condensation appears in cold weather, spread evenly across glass and frame, worst in bathrooms and kitchens, and can be heaviest when it has not rained. A leak follows rain and runs from a defined point, usually at one corner.
A skylight is the coldest surface in the room, so indoor moisture finds it first. Extract ventilation, how the light well is finished and whether the roof space around it has any airflow all feed into it.
That is why the first visit looks at the house as well as the roof. Where the problem is moisture rather than water ingress, attic and roof ventilation is the relevant page, and sealing the skylight harder would achieve nothing.
Repair or replace the unit?
Reflash where the unit itself is sound, because the leak is nearly always in the detail around it. Replace when the glazing seal has failed and the panes have misted, the frame has distorted, or a hatch no longer closes against its seal. The curb is rebuilt either way if it is soft.
Replacing a unit without correcting the curb and the flashing is the common mistake: a new skylight on an old detail leaks in the same place as the old one. If a unit is coming out anyway, that is the moment to raise the curb on a low-slope roof.
Timing with other roof work helps. If the covering is due for renewal, the skylight detail is designed into a flat roof replacement or a shingle roof replacement rather than paid for twice.
Does adding or changing a skylight need permission?
Scope decides it. Resealing and reflashing an existing unit is maintenance; cutting a new opening is structural work and a different conversation with Licenses and Inspections. On a designated property, anything visible from the public right-of-way may also need Historical Commission review.
The Commission's roofs guidance favours work that is inconspicuous from the street, and a new unit on a street-facing slope is about as conspicuous as it gets. One behind a parapet, invisible from the pavement, is generally treated more simply. The Commission confirms for the address.
Outside the city, the township, borough or New Jersey municipality is the permit authority instead. Either way the question is asked before the saw comes out, not after. Our guide on roof permits in Philadelphia covers how the filing works.