By "actually" are you again inferring the requirement for cross over between realities? If the simulated brain was experiencing something, then that "something" is an experience in the frame of the simulation. Or perhaps your argument is that, because WE dont identify the simulated brain as a person its experience is irrelevant?
By asserting that the simulated brain is "experiencing" something, you're assuming it does have qualia.
We actually have no idea how a bunch of atoms interacting create qualia, or even whether they do. There's no math to tell us that a configuration of atoms makes qualia, or what qualia it makes. We have no way of distinguishing between a conscious being who experiences, and a philosophical zombie with the same behavior but no internal experience.
Therefore we can't know whether a simulation of atoms actually does capture what's necessary for qualia.
Sure, I only really know that I have qualia. It seems reasonable to assume that something which looks like me has qualia like me. But if it's a simulation, it doesn't actually look like me at all.
It does have a sort of abstract mapping to something that looks like me, but since I have no idea what produces qualia, I have no way to know whether something essential is lost in that mapping.