That's actually really interesting question and if there are any food chemists on here I would love to hear a detailed answer. I suspect though, that the food energy (which is what the calories measure) stays the same, if you measure by weight -- volume of course can change a lot in cooking -- and were able to correct for water loss/gain in the cooking process. And 100g of carbs no matter what state they are in will still pretty much have the same food energy, as burnt by a laboratory oven.
What might change might be the digestibility, especially what is measured by the GI index -- how fast your body breaks the carbs down. If you look on a GI index site, you will see that cooked foods tend to be higher on the GI index than their raw counterparts -- cooking makes them easier and quicker to digest. (Dr Bronzeager the Archaeologist says: In evolutionary terms, this is a good thing. Fire good! Enable us to get more energy from food quickly so we can run away from sabertooth cat! Also soften food so we do not have to carry around big jaws and teeth like gorilla!)
So the energy from the cooked pancakes will hit your blood faster than if you were somehow able to choke down the uncooked flour and egg and wash them down with the milk. On the whole I think the cooked pancakes are probably nicer.
So I think the answer is, the combination of the raw foods and cooking them is not going to change the calories measurably, but can change how your body is able to use them.
