I gave up after I looked through all the areas and got around 90 flags in the Kingdom. I dont have the time or patience to do it again, especially considering its annoying as **** when you always have to run away, or fight when you past an guard tower.
That is probably the most annoying thing in the game.
But Inner is right, once you restart the game, all your collectibles will have to be redone. I'm assuming that the achievement works when you find all the flags in the game with that save, and not a new one.