Unfortunately, nothing can be done to help that. You see, the two maps are at their given heigts (I'd suspect one is "centered" at 0 meters and one is a DEM at prototypical elevation above sea level). which cannot be changed.
However, if there is nothing on the DEM, or if you have endless amounts of time and wouldn't mind re-creating the original route from scratch--fat chance!--, and have TransDEM, IIRC there is a way to adjust the height within a given range.