"Hello, I'm sure this is all a big misunderstanding, but did you happen to root my computer?"
Not trying to be sarcastic, but I'm really curious what such an email could possibly achieve. If they tell you they haven't done anything, they're either lying or not - you wouldn't know. And really, what are the chances they would tell you that they have rooted your PC if they had?
It'd likely only achieve something if someone else is trying to pull a prank either on him or CSIS, in which case drawing their attention to it might not be so bad (and of course if it's them, they already likely knows he knows, so who cares).
Not trying to be sarcastic, but I'm really curious what such an email could possibly achieve. If they tell you they haven't done anything, they're either lying or not - you wouldn't know. And really, what are the chances they would tell you that they have rooted your PC if they had?