I wonder how sheogorath will be handled. The loss of a deity will be troublesome to the Khajitt...
Sheogorath still exists.
The way I see it, the mortals won't even notice it's not the same guy sitting on the throne. it's kinda like a function if you prefer. Instead of being the new president, you are the new Sheo.
The new guy IS sheogorath and will be worshiped as, without difference.
I have a question though: is it "official" that the new Sheo is the CoC? on aftermath, some kind of canon story comes out but nothing really give us hints about this. could it be a totally different person?
SI was the perfect way to make the CoC disappear though. He saved the world and chilled out a bit, one day a gate appeared, he entered it and never came back.