Leaking skylights can be tricky to fix. You have to remove all of the roofing around them, then the flashing, then the felt, and then you can get down to the root of the problem.

In this case the tile pan flashing was sending the water under the tile roof instead of back on top of the roofing tiles. The result is that the roof wore out below the skylight and they had some pretty serious water damage to the decking.

This video shows the roof all taken apart so you can see what your roofer or you might be getting unto if you're thinking of tackling a job like this.