Do percentages on ingredient lists of cookies refer to pre- or post-baking weight?

This is on the list of ingredients, so it is the pre-cooked formula weight, to demonstrate to the buyer just how much chocolate chunks to expect. Post cooking, the chocolate has changed, as have the other ingredients.

The ingredients also list:

Raising Agents: Ammonium Bicarbonate, Sodium Bicarbonate, Disodium Diphosphate,

These are NOT present in this form in the baked product. They have chemically reacted. The ingredient list is what is used to MAKE the product, not what is left after. That is for the nutritional information.

So, unless this is a US/UK thing, the FDA labeling requirements are clear on the difference between ingredient list and Nutritional information. This is basically (before/ after)

FDA labeling guidelines

This is not unlike ground beef that is customarily sold in the US as 10% fat (very lean) to 20-25% fat (high fat) This is a pre-cooked percentage.

The maker would be hard pressed to do post-baking analysis on the finished biscwit for actual chocolate percentage. Analysis is done for fat, sugar, etc... based on calorimetry and other chemical analysis methods, but cannot determine chocolate percentage after cooking.

Cookies don't lose much moisture in cooking so the difference between 28% uncooked weight and 28% cooked weight is very small. I suggest you make a batch based on the uncooked weight, weigh the tray of cookies just before baking and just after, and decide whether the proportions are right. If not, use the weights to adjust or just think that was too much/too little. The effect of chocolate chips on the bulk texture will be much smaller than the effect of the rest of the recipe, so it really will be only about the desired proportion of chocolate.