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.