I’ve run into this problem with severe dies, mostly Redding. The easiest solution is to use a piece of 100grit sand paper placed on a flat surface (glass or machine bed - I use my table saw) to remove some height from the shell holder. Press the shell holder on the sand paper firmly, while holding the paper down with the other hand, and slide it back and forth slowly without breaking contact with the table/paper or you will round the edges. You can measure progress with your calipers. If you take off too much just adjust your die.