Swapping objects so that object A, which is initially on top of object B, will now be on the bottom after the animation. Natively, PowerPoint doesn’t have such feature to achieve this, though I believe the same applies to most animation tools out there. This however, can be achieved with a neat workaround. First, you have to understand that every shape, text, images and many more, are considered an individual object. If you use Photoshop, Flash or similar tools, think of each object being in their own layer, where they can be rearranged in orders. Objects can thus be sent to the back, bring forward and so on, so as to readjust their ordering. By know this concept, you will then be able to workaround and create a swap animation on PowerPoint.
To do so, you will need 3 objects. Object A, B and C, where C will be a duplicate of object B. Next, re-order the objects so that B will be on top, followed by A, then finally C. Then, add Disappear effect and set it to after previous on object C. This will allow you to hide it at the start. Next, add the same custom motion path on both object C and B such that it creates a swap motion (it should be in a loop). Set the object B to start on click while object C to start with previous. Add Disappear effect on object B, start on with previous and delay to 1 second. Do the same to object C, except with an Appear effect instead. This will allow object C (the duplicate) which is under object A to replace B during the animation.
With further tweaks, you can also improvise the swap animation by having the animated objects shrink during the swap animation so as to apply a more 3 dimensional feel. Swap technique is also an useful animation where you can apply it to various situations. An example would be Orbital animation, which basically uses similar technique showing an animation of the moon orbiting around the earth. Take a look at the link below to see how Swap Animation technique works: Swap Animation PPT