Most often skylights, dormer windows, and other roof openings are added to roofs, so they should be inspected and braced as required. For earthquake loading, this includes checking the opening size against permitted maximum sizes allowed in the codes in seismic zones and removing the skylight or dormer if it exceeds code limits. The framing around the opening—whether skylight or dormer—should be constructed for gravity load requirements such as doubled rafters and headers.
The connections between additions and the existing house should be tied together very well. The level of interconnection should be the same as it would be if they had been built at the same time, or as closely to that as can be achieved.
For wind loads, using tighter nailing patterns and adhesive to secure the roof sheathing around the window opening is an effective way to combat roof uplift. However, the seismic solution is different because gluing the sheathing would not allow some of the desirable deformation in the roof plane. Also, load path strapping should be installed where accessible for all structures penetrating the roof.
Cost will vary, depending on size and scope of roof repair. Consult with your contractor about this and other safety features that fit into your remodeling project.