A file called Track.bin says it is not able to load and I have tried to uninstall this route and redownload it, but it has not fixed this issue and this problem is making it impossible to play half of the scenarios that comes with the route.
It seems there is a folder named "Networks" in the routes folder. This gets created once you make (accidental?) changes to the route. It overrides the contents in the original MainContent.ap. To restore it: Simply delete RailWorks\Content\Routes\00000059-0000-0000-0000-000000002015\Networks folder