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.
The other alternative, which I've used, is to place the route to be merged in a number of baseboards away, and connect the two together using some kind of landscape transition. I did this to bring a layout from zero to 24 meters over 3 baseboards. When you drive the route, you don't really notice the climb too much.
I have got around merging two layouts that are at different levels simply by putting in a portal on each layout, suitably diguised as a tunnel. I have used this to merge the Banks Heath layout with the Glasgow to Falkirk layout. I have added one board between the two and landscaped it to suit the two levels... If the layouts being merged already have portals then its a simple matter of programming the portals to run from one layout to a portal on the merged one. If the layouts have a return loop, the loops are replaced with portals....