I sell low carb muffins, and someone brought up that I can get more accurate value of protein/carbs/cals as well as vitamins/minerals if I account for the loss of those nutrients during the baking process.

Any idea how I find that out?

I don't think your protein/carbs/cals will change, however some vitamins will degrade with heat. I don't think mineral content will change.

I don't think you'll be able to get an accurate estimate on vitamin loss without running lab tests, but here's a link that seems to show what vitamins are unstable in heat. You'd probably have to search some food science/nutritional journals to find out what level of degradation you'll get http://www.beyondveg.com/tu-j-l/raw-cooked/raw-cooked-2e.shtml