Until ya know... CS where the time loop is broken.
Edit: Wooow I totally took your post the wrong way. We're still talking about CT (which makes sense since we don't really know what's going on in CS). Sorry!
Well... I'm think that since the Black Beast is already dead when Jubei trains Ragna so it's possible Jubei didn't know Ragna would become the Black Beast, unless it was stated somewhere and I didn't see it, and Rachel already saved his life and maybe didn't realize he was part of the Black Beast until time started looping? It makes sense in a way until you hit the time loops but I'm thinking of it from the way someone, probably Suzaku, explained the loops. I'd look for it but I don't even remember which thread it was in