Poorly designed or installed flashing creates leaks.
This home has two identical skylights on the roof and one has been leaking. Caulking has been used in an attempt to stop the leak without solving the problem. And that problem is the flashing at the head of the skylight.
Problems are revealed.
As the skylight and old flashing is removed, the evidence of water seeping under the flashing and the damage it caused is revealed.
The process of removal exaggerates it, but can you see the path water took? 
Not the right kind of substructure.
Step flashing integrated into the shingles is part of the solution.
With the shingles, flashing and the damaged pressed wood removed, we first surround the curb with 2′ lumber. This is now a curb that fits the skylight, which is quite a bit larger than the opening.
The next step is to lay down a sticky sheet of ice and water shield. This provides an added layer to help prevent wind and water penetration. It will “glue” the flashing to the curb and roof underlayment.
The next step is, of course, the flashing. Using sheet aluminum and a portable brake, we create custom head, sill and step pieces and then install them as the shingles are reinstalled.
Preparation work is complete. The white is the backing of the ice and water shield and is peeled off. 
The flashing is next to invisible as it fits into the shingles. 
Notice the step flashing along the side. The sill piece lays on top.
Cleanup and a five year warranty on our work complete the job.
