You have 2 options...
Have the roofer fix the roof flashings around the skylights or whatever the leaking issue is and then enjoy the skylights (maybe $100. each if the fix is just replacing the flashing and shingling around the lights)
or...have the roofer remove the skylights, reframe the opening, new wood over opening, repair shingling. That could run $200. or more per light.
If the roof shingling is in bad shape all over, the roofer would want to redo the whole patio roof's shingling at that time. Add $$.
For a roofer it is an easy job. He will remove the skylight and fill in the hole and roof over it. It might be easier and cheaper to have someone fix the skylights.