Why do you duplicate your level if it's to merge it back?
Duplicate a level is very easy. If your level is a scene, just save it as a new file, so you will have two files containing the same scene separately. If your level is only a branch of a scene, you can right-click on the branch and choose "Save branch as scene".
However, if you use one of these two solutions, modifying the original scene will not update its copies. Because of course, they are copies^^
So if you want that, a third solution is to choose Scene -> New inherited scene.
This will do the same as saving under a different file, but instead of copying, the new scene will refer to the original. Changes to the original will then replicate in the inheriting scene, unless you made changes to it, which will individually override the original.
Scene inheritance is mentionned here: http://docs.godotengine.org/en/3.0/getting_started/step_by_step/ui_game_user_interface.html#use-scene-inheritance-to-create-the-remaining-elements
But I believe you have to read more the docs because it's part of a tutorial.