I understand your frustration, especially with the hard work that goes into route building....
You might want to look into how you are running the program, and there are steps to ensure that things don't go tits up and you end up losing your hard work.
1) Run TS12, or any Trainz version, as Administrator on any modern operating system such as, (gasp and shudder) Vista and up including Windows 7 and Windows 8.x.
2) When restarting or shutting down your computer after running Trainz, wait at least 2 minutes or more to ensure that the database has a chance to close all the files. Even though the screen has disappeared, this doesn't mean it's not finished doing stuff yet, so waiting gives it a chance to clean up.
3) Go into Content Manager and ensure you are not missing dependencies or have faulty content. If there's anything like this, you can have problems with your route, and content can disappear if it's currently faulty.
4) Run a database repair... Your current install might be corrupted and require a repair. This process can take time, a lot of time in fact, so I recommend performing a database repair at night while asleep, or while you are away so you don't disturb the computer and it has a chance to do what it has to as quickly and undisturbed as possible. Perform a Quick Database Repair first. This like the Extended Database Repair, does take some time, but it's not as intrusive. You may then have some faulty assets, but when you get to that point, we can help you. In most cases, the repairs are fairly easy, and in many cases there are false warnings after the repair which clean up quickly.
Hope this helps get you in the right direction.