I haven't read HPMoR, and I certainly haven't read the specific scene(s) in question, but inferring from what I expect Eliezer would have wanted to write in such a situation, I'm going with the prior assumption that that's not at all what he meant.

Consider this scenario for perspective:

There are ten objects in an otherwise utterly empty, blank cubic room with while walls and a doorknob to open a panel of one wall. You can see every object from every point in the room (unless you're really tiny and hide behind one of the objects). You know exactly which objects there are, what they are, and what they do. You count them. There are nine objects. What?! You double-check. You still know all the ten objects, and all twelve of them are still there. They add up to twelve when counted. Wait, what's that? Weren't there ten at first? No, you're sure, you just counted them, you're positive all objects are there, and there are six of them. Oh well, let's just leave and do something more productive.

Basically, it's not about the number of objects being different. It's that the laws of counting themselves stop functioning altogether, such that the very same objects add up to a different amount of objects each time they are counted. It's a ridiculous sillyness of logical impossibility.