Hi Paul,
Bernie is correct. Trainz Map will change your tracks for you. Just make sure you have SP1 installed if you are using TRS2006, and the current version of TrainzMap. This fixes a bug that caused TrainzMap to fail when the track was selected.
There are a couple of additional things that I would like to mention. You'll need to disconnect and reconnect any track to interactive industry objects such as stations, industries, etc. that change their track when a spline is connected to them. The reason is that they will not change their track when TrainzMap changes the track around them.
This program will not change bridges or double-track. These objects are different than fixed-track industries so they are not affected by the track change.
John