I just had this thing disappear for the third time !!! Could changing the "Environment" (sky, month and time of day) be screwing this thing up? It is a shame, because this is such a beautiful route. I added one locomotive, twenty five empty coal gondolas and then changed the environment and "saved as" with a new session name; exited surveyor and it is NOT in the route list any longer. This is BS man !
Check Content Manager and see if there are any errors first before we do something else.
Are you running as Administrator?
When you run Trainz TS12, run as Administrator. Right-click on the icon and choose run as admin when you start. You'll be prompted to click on something - click on OK. The program will load.
This will ensure that whatever you are doing is saved properly and that TS12 has user rights to the folders.
The way you're working maybe created some confusion. This has to do with not you, but the way the layers are implemented in the program. Layers are there to allow you to create multiple sessions using the same track layout, but change things such as Trains, Environment, and other variables.
What I do is to never put anything on the route-layer that should not be permanent, including trains.
You will notice that when you save something to the route layer, you'll be prompted to save both the route and a session that goes with it. When I save a route, my first save is a Save as... and includes saving the default session. After that I do not save a session while working on the track layout, adjusting things, placing assets, etc. When it comes time to setup the running session, I create a new session. In there I place the trains and setup running schedules, etc.
Now to make things a bit more complicated, you can place objects that only appear in a session, but are part of a route. This can be such things as trees, buildings, and other objects. You can move items from the route layer to the session layer within Surveyor. This is helpful, for example when you are editing a route and want to keep something from moving such as people sitting on a park bench under some trees. When you go to move people, the trees get in the way. By locking the trees, or even hiding them, you can easily move the people around. When you're done, unhide or unlock the items by moving them back to the route layer.
Experiment with the last part to see what it does for you. In the mean time, keep things simple like I do. It makes the world of difference when it comes to stuff like this.
John