I'm assuming you have a version of AS that supports animated layer ordering...(e.g., ver. 5.6 or later). It's easy. Place the folders you want to swap over into a Group Layer (you can use a Bone Layer too), and simply drag the layers around at whatever point in the animation. That's it.
Note: This isn't a "Bug Report". It's a "How Do I?"...
You can't have everything. Where would you put it?