If you have to replace shingles around a skylight, examine the old flashing. Most residential skylights sit on a raised curb made watertight with metal flashing. If it’s carefully removed when the old roof is torn off, it should be reusable. If not, you’ll have to buy new flashing ($50 to $100) either from the skylight manufacturer or from a roofing company that has a metal fabrication shop (look under “Roofing” in the Yellow Pages or online).
First remove the skylight’s counterflashing. On some units, you have to remove the whole glass frame (lead photo below). On other models, you simply unscrew a metal channel from the curb. Next pry off the old shingles, carefully pulling nails to save the flashing. To reassemble, follow the steps as outlined by the photos, and you’ll have a leakproof installation. Note that the metal flashing pieces don’t need to be sealed to each other. Since water runs downhill, they only need to be installed in the right order. So put away that roofing cement.
If you’re hiring a roofing crew, ask them to carefully remove the old flashing and reuse it if it’s in good shape.