in your project, set the stock thickness to the thickness of your thickest piece of stock.
If you use this on a piece that is thinner, then you will get some air cutting. You can decide if the air-cutting or updating the file is more annoying.
If you still have difficulty, please post photos of the stock you are having difficulty with, the file you are trying to make to cut it, and let us know how you are setting zero relative to it.