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.
I tried recreating this style of recipe card and ended up using a JSON tree structure to store the recipe. I also added fields for a little more description so that I could generate a little more traditional lists for ingredients and instructions.
https://git.tilde.town/gamerdonkey/recipes_for_engineers/
Example recipe: https://tilde.town/~gamerdonkey/recipes/lemony_olive_oil_zucchini_bread.html JSON representation: https://tilde.town/~gamerdonkey/recipes/lemony_olive_oil_zucchini_bread.json