Until the wound becomes a window

Like. Beldaruit loves Qifrey. There's no question of this. Just as there's no question that Qifrey's life is undoubtedly better because Beldaruit took him in, and he obviously respects him a great deal. But Qifrey has never been able to fully trust Beldaruit, and for good reason.

One thing that keeps me awake at night is that chapter 38 strongly insinuates that Beldaruit knows about Treefrey situation. Chapter 59 suggests that Beldaruit knows more about Qifrey's secrets that he lets on.

And I think we all agree that all of Beldaruit's cards are not on the table yet.

I do wonder if he wanted Qifrey to become his apprentice because he figured out the tree-situation early. Or maybe he figured out what happened to Qifrey after Qifrey was already living in the Great Hall. In any case he never talked about this with Qifrey.

As you said, Qifrey was allowed to become a witch because there was no sign of forbidden magic on his body. Beldaruit admitting, even to Qifrey only, that he knows the truth would only show more hypocrisy and problems Witch Society has.

And yet when Coco is hurt, Qifrey goes straight to Beldaruit. He asks Beldaruit to have an eye on her. After Easthies' accident during Siver Eve arc, Beldaruit wonders where Qifrey is because Beldaruit knows he can rely on him.

That said, I do think it's pretty unlikely for him to have known from the start. Qifrey is, as far as we know, the first attempt at this specific kind of forbidden magic - he slipped under everyone's radar because no one knew it was possible, and so didn't know what kind of signs to look for. Bel was also fairly young when he took Qifrey in and wasn't a Wise yet, so it seems like a stretch that he would have just guessed 'Silverwood parasite' off the bat. Seems more likely to be something he pieced together over their many years of living together, particularly after it fully sprouted at the Tower of Tomes and Qifrey had to start worrying about it being an on-going problem.