A couple of weeks ago I saw a documentary on some TV channel--probably the Smithsonian channel--that was originally intended to be a typical "this is what it is like on the reef and the nearby area" show. By coincidence, they were there and filming when the cyclone arrived, and that became a key part of the show. They were able to show the devastation on the land pretty well.
What was most interesting though, was the section in which they showed Google Earth filming the reef. Yes, seriously. They used divers pushing a really cool camera that took video in all directions, including up and down. The Google Earth people had been working on the reef just before the cyclone arrived, and they went back after it. The show included one before and after clip that showed MAJOR damage. It went from a beautiful, colorful reef system to a pile of white rubble. Of course, that was only one site, but it showed that the reef did sustain damage that will take a long time to recover.
Yes sites vary.
I heard RR 9-10 area got hit and the Lizard Island Research Station staff blogged about damage in sites there. So as this was a charter we chose not to go there. Lena Reef and Turtle Bay (near Tongue) had damaged areas, not sure when. I did not go in at Horseshoe Reef but my friends did and saw Crown of Thorns, very sad.
I am grateful I got to go one more time to see great beauty at GBR. It is just amazing and humbling.