Warning: more philosophy!
A simulation of a storm is not a storm. (The storm is wet, but the simulation is not.) A simulation of the calculation of π is a calculation of π because it achieves the end of computing π. Both storms and calculations are physical processes and we thus have two categories of physical processes. I am inclined to put what the brain does in the category of calculation. In this sense a simulation of the brain does whatever the brain does, at least at the level of brain inputs and outputs.
From this perspective the simulated brain feels pain if the simulation is sufficiently faithful to respond in ways that would cause us to say that a real brain ‘felt pain’.
There is another transformation on a process that may sometimes be performed. Technologists speak sometimes of a ‘technology translation’ where some process, typically artificial, is systematically replaced by another process which can be seen to be isomorphic to the first. I first heard the phrase when computer designs were translated from vacuum tubes to transistors. It is not precluded that natural processes might be translated to artificial technologies. The relation between the new and old is more symmetric in case of a translation. I put it in the simulation category however.
Yet another category of transformation occurs when a computational process is discovered to be equivalent to some new simpler computation. There is no reason to believe that brains can be much simplified.
I put more store in a farmer’s ontology than a philosopher’s. He may speak of next year’s seed corn and have in mind a specific set of bags of corn and his plans for that corn. Then a specific set of atoms is under discussion. He may also speak of preserving a species of corn for his children when they inherit the farm. In such a case it is not the atoms that are to be identified, but a pattern that those atoms may fall into. He may teach his children how to decide when to plant. This is a process that may not have a name but is the sort of thing of which culture is formed.