But, you can't spot-reduce fat. You have a body fat percentage throughout your whole body, you can't have less fat in your arms than your stomach although everyone stores fat slightly differently and an "apple shape" (male) will always store most of their fat in the stomach region.
Also, isn't cortisol related to stress? If so, running helps relieve stress, at least I think. But, if you're running on fumes, I could see it increasing those cortisol levels... guess everyone is different.