I want to thank everyone for the help. I did opt to cut the roof rubber and peel it back. I had to remove a section of old wood roofing and to firm up the whole area I ran a 16 gauge sheet metal to help secure the new wood. The wood is in and screwed and glued down and tomorrow I will use 3m rubber glue to reset the rubber roof onto the wood. Then on Tuesday the eternabond tape should be in so either Tuesday or Wednesday I should be able to have it secured to the point I can put the original skylight back in this week. Again thanks all for the suggestions and I ended up learning how to replace wood on the roof.