Thanks for writing! You can avoid duplicating the Application-as-recipe if you duplicate the project prior to converting it to an app. For example, you would create Project A, duplicate it (Project B), then convert Project A to an app-as-recipe and begin using the recipe in Project B. When you continue duplicating projects from there to use as templates, you should not see any duplicate recipes.
In order to remove the duplicate recipes, you will want to delete the duplicate projects (Project > Actions > Delete), then clear your browser cache.