Yes, the literature on this bad. It's even worse than that. Metabolic adaptation means you may think you burned 400 kcal with a long run according to the tracking app, but maybe your body, on net, only burns 100-200 kcal, so this throws off the math.
Now you're just making things up. On any training plan, a long run would be a minimum of 6 mi / 10 km. No adult is going burn less than 400 kcal over that distance, it isn't physiologically possible. And any metabolic adaptation will only be a few percent at most: running economy only improves slightly with training.