How to change elevation of an exsisting route.

Hi! I have made a rather large yard and about 50 miles of mainland track, some of which is in fairly rough terrain. When I merged new tiles by overwriting existing tiles, the overall height of the route decreased from 1 to 3 meters. I don't think the leveling tool will do the job, as it would spoil the terrain effects. Is there a way to correct this by amending the route .bin file or blueprint? Unfortunately, I didn't do a backup at that point not realizing what could happen. Any thoughts? Cheers; Chuck F