Another typical replacement.
We have replaced quite a few of this brand of tubular skylight over the years. With a lens that is smaller than the tube and opening in the roof, it is a rather poor design to begin with and should probably be replaced whenever a roof is being replaced.
As can be seen in the image above, caulk has been applied in numerous spots in an attempt to stop leaks—not a good sign!
in the process of applying ice and water shield, including the nearby roof jack. 
The Velux Sun Tunnel is a far superior design.
All Skylight Specialists Velux Sun Tunnel Replacements have a 5 year no leaks workmanship warranty.