Nothing to worry about, they'll have their happy end and they'll continue to be friends with Will. Daath is just confused about the reaction of his body, because he doesn't understand why it didn't reject Will. And now he feels like he betrayed Juda and he doesn't want to tell him.
I'm reading both this and Petit Mignon so I'm a little confused... In this story, Juda and Daath still have no babies right?
Sooooo.... We have no reason to worry really... Because they have a lovey dovey future ahead with their babies right?