Does "substituting x for y" mean "getting rid of x and using y instead", or does it mean "getting rid of y and using x instead"? To me, it means "getting rid of y and using x instead".

Oh that’s interesting. I can see your point. I guess it’s a bit ambiguous and can mean either thing. As the other responder mentioned, the backwards construction in the original sounds like 19th century literature, and from context I know they mean removing x and adding y. But in another context it could mean the opposite. Thanks for pointing that out!