Your routes and other stuff should be fine, these are located in Local and Packaged.
The Local folder contains everything you have downloaded from the DLS, the Packaged folder contains all of your purchased content and of course the Original folder contains the default content 'Don't mess with this folder'.
What you need to do is:
1) Launch Trainz
2) DO NOT launch the game
3) At the top you will see some menus 'File, Edit, Developer'. Click the Developer menu and choose 'Rebuild Database'.
Allow Trainz to rebuild the entire database and everything should work normally.
If however, if didn't work.
1) Back up the following folders Local and Packaged; ONLY! Do not back up anything else.
2) Uninstall Trainz, then restart your computer
3) Reinstall Trainz
4) Ideally, your backup of the Local and Packaged folders should be archived in a 'Rar' file. Extract this to your Local Data Folder. Overriding the current 'Local and Packaged' folders.
5) Launch Trainz, then at the launcher Click 'Developer' then Rebuild Database.
Everything should be fixed.
A solid warning! DO NOT backup
Backups
Cashe
Editing
Libraries
Original
Optional: Backup Screenshots, not really needed unless you have some good screenshots you want to keep.
DO NOT backup any files with '.tdx or .dmp'
Hope this all helps, best of luck