When I create a new route and save it, I give the route a distinctive name and the session a distinctive name (NOT "default"), From that point on, whether I am editing only the route material (track, trees, etc) or the session material (consists, industry properties, etc) I always load and edit the session.
If I have altered something in the route only then when I select save Trainz will ask if I want to save the route and session. I select both Overwrite existing route and Overwrite existing session because it is possible that I may have altered something in a session - in a long editing job anything is possible. This will not create a new route and session but will overwrite the previous versions with new versions.
If I have altered something in the session only then when I select save Trainz will ask me if I want to save the session (not the route). I select Overwrite existing session and only the session is updated.
Of course, if I have altered both the route and the session then I select both Overwrite existing route and Overwrite existing session.