Linus,
The old skylight hole must be covered with decking material. It must be the same kind of decking that is on the rest of the roof. My guess is that
it’s probably 1/2" CDX plywood (CDX= Rated for exterior use). All professional roofing organizations recommend that the plywood be replaced in whole sheets only. What I mean is… don’t just cut a piece to fit, you need to replace the entire sheet. It has to do with maintaining the structural integrity of the roof. Then the roofing material can be re-installed over this area.
As to the trusses being upgraded for this skylight area, I would recommend that your client obtain a structural engineer’s signed paperwork stating that
the area in question was repaired or upgraded to his/her specs.
Trusses can not be retrofitted without a PE authorization.