There's a built-in function in TransDEM to remove the TransDEM ground textures. You'll find it under the main menu, "Trainz" tab, "Remove Ground Textures" command. As usual, route has be opened for edit with Trainz Content Manager. The function will remove the standard set, a specific texture KUID or a list of texture KUIDs specified in a file, e.g. the TransDEM ortho-image textures. If a TransDEM texture is the only remaining texture for a particular ground vertex, the default orange/grey grid texture will be used as the replacement.

Won't work yet with a T:ANE SP2 route, I'm afraid, due to the changes in route Trainz file formats (now per baseboard for .gnd, .obs and .trk plus some new files and a few other obstacles). You should get an error in TransDEM when trying to apply the ground texture removal function to a T:ANE SP2 route (which must be opened for edit in T:ANE Content Manager, of course). I'm still analysing and adapting to those changes, with some progress made meanwhile, but it is slow and will take time.