I don't know the actual reasons for him being out lately, but I know he's been on vocal rest at various points in the run, and some of the notes in his songs were lowered a while back. I can't imagine how he gets through the physical demands of the role along with everything else. 7 months of that is intense. Even when I noticed he was sick, he was still giving 110% on stage, so it absolutely has to be taking its toll.
I noticed they are dropping Sunday evening shows in favor of Weds evenings, perhaps it will be a better schedule for him.
I am rooting for him for the Tonys, so hopefully this isn't detrimental to his chances, as he's phenomenal.