When I met him at the Public, several people asked whether he'd be making the transfer. Looking had not been cancelled, and so he said he'd have to wait and see what would happen with Looking, but being in Hamilton was the most fun he's ever had in a show. I've also read interviews with him where he said he will stay as long as they will have him, and talked about how much he loves being in the show. That is probably an exaggeration--I'm sure he'll leave eventually--but with his seemingly genuine love of the show and its immense popularity, it wouldn't surprise me if he'd stay longer than you'd otherwise expect him to for a relatively small part.
I also thought I read somewhere that they gave him the option to take a break from Hamilton to film the Looking move and then come back, but I don't remember where I read that, and we all know not everything on the internet is true....