No it doesn't, you must be confusing your routes. The duplicate is named the same as the original but with a 1 at the end. If you change that the original remains unchanged.
Are you running the current version of BaseCamp? It should be 4.1.1.
You can check by going to the Help menu and picking "About BaseCamp".
Are you seeing the prompt whether you would like to duplicate the waypoints when you duplicate the route?