It appears you are not distinguishing between the substance and appearances or accidents of the bread and wine so that no change actually occurs in the nature or substance of the bread and wine at all at their consecration.
Perhaps it is a different perspective on the “matter”. Or maybe, a post is insufficient to go into all the specifics. Likely both.
We can say that in this case and generally, what does not change is the fact that something exists. The other aspect of anything that exists is that it is brought into existence and known by God. These would be the foundational realities of creation. The ultimate Ground is God who brings all that is into existence through an eternal act of Divine will.
Let’s see if this makes sense:
What exists before it is transformed into the Eucharist is a wafer. It is comprised of molecules which are one in its existence as a piece of bread. That is what it is in reality and how we can understand it. We can isolate its atomic structure subjecting it to physical processes, such as heat and acids, which act on that level.
Let’s now consider ourselves. We are material beings, having a psychological and spiritual structure. Our perceptions, thoughts, feelings and actions exist through our participation within the physical universe. Damage to different areas of the brain will affect the corresponding capacities. We are able to know and act because the person is fundamentally a unity - individual being existing in relation to what is other. We can lose a limb, an eye, our memories, but the person, although diminished in his/her capacity to express him/herself remains as he/she is created and loved by God.
The Eucharist is different in that every part has become the body and blood of Christ. This is what it is and can be understood only through faith. The glucose and other molecules that make up its physical structure are real - created by God. These can be understood as being accidents, a reality which can be discerned, but is merely the appearance of what is in its totality. The reality of the host which goes beyond the physical and psychological (what it may symbolize), is its spiritual existence - its beingness as the body of Jesus.
The “substance”, the reality of a thing is what God says it is and would include the being of its components which I see as being one within it, the physical structure that allows for it’s being perceived, ingested and digested. The reality is that of the Eucharist. Atoms can be thought of as information or ideas that exist. That information is not lost as it is incorporated into a new substance, a beingness that is one within the Trinity itself in Christ. Existence itself is one with that which it brings into being. Through the Word, His becoming flesh, His death and resurrection, and our eating of that flesh, we are able to journey on that Way, as we become body and soul, Christ-like.