^ It's probably a bit more tricky than simply replacing him. Who wants to be the production that fires someone who has been through as much as Javi when he's doing the best that he can? I can see the articles, statements, and interviews now. What a headache. That's a bit business minded, but with all the actor blog posts, and tweeting, and blah blah blah, replacing an actor with two terminal illinessss and an injury based on an attendance can be very merky territory.
To another end he's friends with Lin. He's an original Broadway cast member, maybe Lin and the producers are being empathetic to him given his relationship to the show and his circumstances.
Lastly, he's quite sensational in the role when he is there. I wouldn't be surprised if the quality of his work when he is present outweighs his absences. I don't think many non theater people are going to see him in the show. There are cavalcades of people who would see Hamilton with anyone in any role.
His personal circumstances, relationship to Lin and the show, and lack of audience disappointment/effect on the the box office probably all weigh in ultimately making it either a preparable or non issue for production.