It would just need to _look like_ it has an effect on the simulated brain, right? If you ask me a question and I pause, say "hmm", and put my hand to my chin, can you know that I am actually thinking and formulating a response? If the entirety of your observations are external, of course you can't. There is no way to tell if my response is a random choice from an array of preset answers, or a group of concepts activating each other.
That's because brain activity is part of what our inner, first-person experience looks like from a second-person perspective (ie, an external observer). Tears are not sadness, they are what sadness looks like, they are an external description of an internal state. Sadness can only be experienced by the person experiencing it. Tears are a description of sadness. But can't tears be faked?
So when we see the same neuronal activity in both brains, we have no way of knowing whether inner experience actually gave rise to the activity, or it just looks like it did.