I ran into this exact issue when I was making these diagrams for my own recipes: https://git.tilde.town/gamerdonkey/recipes_for_engineers#known-issues . My workaround was just to have instructions to set some aside and use it later.

I find this layout works best for in-the-moment reference while cooking, and the 2-dimensional nature of it is what really makes it useful. So I think of splitting an ingredient as like lifting some of it out into an imaginary third dimension before inserting it later at another step.