Or, you could try to fix it;
http://forums.flightsim.com/vbts/showpo ... ostcount=8Kitbashed one of my early railsim routes into a DEM template using that method, since track and scenery objects don't work and play well with each other I did first the track, then the scenery;

Whole smash underground, so I exit, delete the scenery folder so nothing is left but the trackwork.

With track you can drag a circle and select a VERY large area, if you can't see the gizmo just hold down the V key to raise it, press SHIFT to go up faster. Scenery objects actually didn't work as well as the track did, I had to copy and paste individual .bin files in and out for that, four tiles at a time. Raised the track and then the scenery 300 meters to get it near the elevation of the new route, beta available here;
http://www.humyo.com/F/9455455-638257003Still requires some cleanup work like chasing down buried switch levers and reconnecting turntables, but it beats doing everything you've already done over again. Haven't really tried merging two different routes complete with track yet, but a brief study of the tracks.bin file shows that would probably be rather complicated.