Skylights should be removed during re-roofing, and re-installed so they are fully integrated as one system with the new roof. If you are getting leaking after new shingles are put on, you can do a test yourself to determine what the issue is. Go up on your roof and wrap your skylight in a tarp, using straps to secure it. Then run some water down your roof. If it leaks, you know there is a problem with the new roof – very likely that roofers did not remove the skylight and properly put the roof membrane over the skylight curb, which is part of the skylight frame that makes it one system with a roof. If it doesn’t leak there might be some damage to your skylight and it might need to be replaced. Either way, give us a call and we’d be happy to come do a free inspection.