Good question!

I think if you do that the little red light would stop blinking and you'd break the internet.

Honestly I'm not sure, I'm also quite new to the fediverse. My guess is that being a parent comment, B wouldn't see it, but if C was the parent and A the child comment, B would see only C.

Federation is by definition a union, a mutual agreement. A and B are either federated or they aren't, there is no "A is federated with B but B is not federated with A".

So if A and B are federated and B and C are federated but not A and C, and your scenario happens, the person on B sees your comment but the person on C doesn't see it and can't reply to it.