It's a non sequitor - we're talking about hypotheticals which feature entirely different physical structures, or similar physical structures composed of physically distinct sets of atoms, not single spatiotemporally connected sets of atoms. We are talking about instance identity (the "same" mind), not categorization.
Of course, it's not a non sequitur. We already know that the human brain changes substantially and structurally over time (and that we can change it further by meddling). Similarly, experiences and connections with other people radically change the human mind. Meanwhile there is considerable flow of atoms in and out of the brain just due to normal biological processes. I believe the mind and brain are just an example of the Ship of Theseus (a mythical ship which was supposedly kept sea-worthy over many centuries by replacing it piece by piece so that at some point, it no longer had any piece of the original ship in it).
The brain and mind changes, hence, it is relevant, especially in a thread on humanity's future capabilities in AI on how far we can push that ability to change in order to improve the current versions of intelligence.
Also, it's worth noting that if one is to speculate about future human or AI capabilities or traits, it is very natural and useful to speak of hypothetical situations, not because they are likely to occur, but because they illuminate possible general concepts, outcomes, or problems. Sure, this particular hypothetical might be unlikely to occur, but I believe sooner or later we will be speaking of actual transformations of the human brain and mind rather than hypothetical ones. And I believe such transforms may become quite radical. So it is interesting to consider just how much can you change the brain without changing the mind it implements or whatever.
Moving on, "instance identity" is a categorization by you. In fact, categorization is by definition a coarse identification which when applied to instances or representations of some abstract thing becomes by definition an instance identity. Sure, normally, we think of identity as the minimum unit of distinguishability. But we can distinguish bodies, brains, and minds even over the course of minutes. By reading this post, you have a different brain and mind than you did before you read the post (should I apologize for that?).
You are begging the question, by simply assuming that human mental processes are exactly representable in entirely different physical structures.
Which is not a serious problem here. After all, we already have a working instance of human mental processes, the human brain with no obvious connection to what materials the underlying machinery is composed of. It's like claiming that a car won't drive, if we make it out of aluminum instead of out of steel or the wheels of wood not rubber. Sure, if we have a ridiculous amount of failed effort put into the problem of changing the structure of the brain and mind at some very distant future date, then maybe you're right. But I don't think that will happen (especially given how easy it is to change the human mind now with education and experience).
I think rather the real difficulty will be that the human body, due to its evolved nature, is extremely difficult to reverse engineer and a key direction of effort will be refactoring of the structure of the body and mind on somewhat more manageable directions.