It changes substance: what it is (as contrasted to how it appears.) Substantia. Hence the word.
If a person does not believe in the existence of things invisible as well as visible, it’s hard to see how they could be alive at all to spiritual realities taught by Judeo-Christian revelation. But perhaps you don’t claim to be.
But you already said it didn't. Quoting you, it doesn't change "weight, molecular structure, chemical characteristics". Those things aren't appearance, they are substance. It doesn't get any more substantial than "weight, molecular structure, chemical characteristics".
"If a person does not believe in the existence of things invisible as well as visible..."
I believe in lots of invisible things, because there is evidence of them. But I don't believe that something both does and does not change at the same time. That's just silly.