I don't have TANE, but looking at your station stops and remembering my own jump from TRS2004 to TS2010, my guess would be layers. Unless you pay attention to those you may think you're placing buildings in the route layer when you're actually working in the session layer, then all the buildings are gone without that session. Some say you should always edit a route through the session and merge layers, I prefer to edit a session separately from editing the route, and always exit back to the menu when changing which one I'm working on.
