OP, did you ever get this Skylight issue fixed?
When I looked at this thread, it seemed to me that you needed to replace Vent Covers. In the first picture above, the Vent Cover is the open "Lid", hinged at the right in the photo. They're easy to replace. Disconnect the arm that lifts them when you turn the crank. Open the Lid till it's over backwards. Then something has to be loosened, removed, straightened, to let you slide the cover out of its track to one side or the other, then slide the replacement in. Then tighten, replace, bend back, whatever retains the lid.
I can't be more specific because there are about three versions of the Lid. Camping World has pictures of the types so you can figure it out from there.
The standard ones are inexpensive, less than $20, and there are Lexan ones that might be say $30. Worth it in the Southern Sun. So is putting Vent Covers over the whole assemblies. They protect the Lid and also allow you to have it open in the rain. I have them on all three of our vents. They look sorta like an A/C shroud, and I know you know what those look like. MaXXair is a popular brand, but Camco and others offer them as well.