Sorry to say but, I think you're in quite a pickle..

Being an experienced route builder, the only thing I can suggest is to lower all the tracks manually, within the route editor. The z co-ordinate (height above sea level) for your terrain tiles cannot be changed through hacking them. Serching through countless track tile files looking for the height above sea level for each of your track sections would take weeks. The quickest approach would be to use your tracks existing gradient points to lower the track to the terrain.
Select a gradient point then press L on the keyboard to lower it to terrain height.
You would then have to regrade some sections where needed. Sounds like a long process but it's a faster solution then editing "bin." files, wich can do more harm then good if you're not careful.
You might want to consider backing up your route before making any radical changes as well. It's been a life saver for me on numerous occations.
Hope this helps and good luck

The word?..The word is no. I am, therefore, going anyway..