If they ever leak, can you remove the frame from the housing and replace/repair it without disturbing the roof? A roofing contractor is pointing out that they will eventually leak, and it would be a good idea to replace them along with the roof. I have no doubt about them eventually leaking, but wonder if it could be fixed without disturbing the roof. I think he is trying to pull a CYA at the customer's expense or just running up the bill.
I have 2 other quotes on the roof and the contractors didn't say anything about the skylights. There are 8 of them for a total of $4,800.