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 skylight

2) 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?