Sure, changes in elevation will naturally mean you burn more calories.
The bit of uneveness on a typical trail doesn't really make any appreciable difference. A trail that is significantly tilted sideways (eg. going around the side of a hill) will burn more calories, as a number of muscles are working to keep you balanced and upright.
However, one thing to watch is that a trail that is challenging enough to burn more calories, is probably going to lead to you slowing down. You may want to check the distance and your timings to ensure you are in fact holding the same speed.
The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore all progress depends on the unreasonable man.
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