Start with the weight of besan used in the batter. After cooking, divide the total protein from the besan by the number of roughly equal chillas.
Try it with your own recipe
If your pack lists 22 g of protein per 100 g and you use 100 g of besan for four equal chillas, that is about 5.5 g of protein from the besan per chilla. Estimate any paneer, tofu or curd separately.
Use it to plan breakfast
Note how many chillas you usually eat and whether you have a side. That is more useful than copying a figure for one chilla from a recipe that uses a different ladle or pan. Five egg-free breakfast ideas · Indian Food Composition Tables
What if the chillas are different sizes?
Use the same ladle for each chilla if you want the estimate to be reasonably even. If the first chilla is small and the next two are much larger, treat the per-chilla number as an average. When adding chopped onion or tomato, keep the besan calculation as the starting point. If a filling is important to your comparison, weigh the amount you use in the whole batch or in each chilla.