I am looking to get a new roof soon. It is approx 20 years old ( 2 layers on roof now), as well as the 2 skylights. The skylights are in good shape and do not leak. However, whoever installed the skylights ( prior owner of house) had put them on top of the old shingles (instead of the plywood sheathing), then the new roof was placed afterwords. So I have 2 questions.
1) If the skylights are in good shape, should I just leave them? The inside is boxed in finished sheetrock and it will require tearing it out to replace the skylight2) If I keep the skylights, will the skylight flashing pose a problem with the new roof since it is resting slightly higher on the old roof and sheathing?