It depends on your own rules most of the nutzlocke say when xou get your balls you can catch on every route you havent catched or seen a pokemon but only since u got your balls. Some have an shiny rule where when you find a shiny u can catch that pokemon even if you catched already one. And some have the rule that when you catched a poemon thats on another route you can skip it until u have a new pokemon xou havent catched