Prayer flags are suppose to tatter and fade. As they are worn by the wind and other elements, that's the prayers being lifted up to the heavens. If there is even a piece of a prayer flag left, it is supposed to be left, because some of the prayer remains. Throwing away a partially-worn prayer flag is the equivalent of throwing someone's prayers away. Of course, the flags around Disney's Asia don't have actual prayers on them so as to not be offensive. They're just printed with animals and various symbols. Still, the tattered flags are correct show.
When I saw the new ones in the video, I thought about this as well, but hesitated to say anything. The new ones just look too new to fit in with the story. They should have been "aged" a bit before putting them up. I know in time they will, but right now they just look a bit out of place.
Looking back at some of the videos from when it first opened, they appeared to be properly aged. Somebody just messed this one up by being lazy.