With LTP subs, the channels that are included in the scene will change and any channels not included will be unaffected. When you first build the scene, make sure every channel you need is in the scene. You can do this by first clearing out all channels (hold down black). That way you know that what you see will be included when you save the scene.
If a channel is set to snap after fade, it will change color or whatever it does only when the sub fader reaches the top. If the fader doesn't hit the top the color won't change. After the fader hits the top, when you pull the fader back to 0, the channel should go to 0 or off. If you start a new sub before pulling the old one back, the new scene will replace anything in the previous scene as long as it's included in that new scene.