Ah, you yourself are falling into the old failings of combating materialism: Using materialist methods and materialist measures. Trying to prove materialism wrong with materialist frameworks is a fools errand. Like mentioned above: it has failed time and time again, and I'm fairly confident it would fail in your example.
If the argument is "X isn't encapsulated in the material" then surely removing the material should leave X intact. The other option is experimenting on what actually encapsulates X, but non materialists have a tendency to say what actually encapsulates X cannot be interacted with nor observed.
Yet they somehow claim that the non interactable non observable stuff is the actual mechanism by which things work. Which begs the question of how they reached that answer to begin with... since it's non interactable and non observable
Unless you got good reason to believe that there is more to it, you don't attach additional meta proprieties that no one can investigate, even from first principles (and this part is important, because it could be that the investigation methods simply haven't got there yet)
Howso? What alternative is there that still uses logical, if albeit not materialist methods?
1) Try materialism over and over again anyway hoping it will eventually solve the problem.
2) Develop a new discipline starting with the axioms of the problem at hand.
Number 1 has been so successful and provided so much work for scientists that any problem it doesn't work for mostly gets ignored.
I'm not saying materialism is necessarily wrong or bad BTW, just that it has a limit. It starts and ends at the perimeter of shared *human* experience.
If, on a hypothetical example, we could come up with an experiment where you removed half of 100 people's nervous system and most of them kept acting like normal then the scientific method would "prove" that materialism isn't correct (unless, of course, someone came and found out that what actually makes people behave like they do isn't their nervous system).
There is nothing making the scientific method unable ascertain whether there is more to the universe than the physical things in it. The scientific method just fails again and again at reaching the opposite stance.