The short answer is no. The slightly longer answer is not really.
The full answer is that you can't change a shape, but you can replace them. Unfortunately, because the physics engine has no idea how the surfaces involved are moving it's going to cause the collision to act a little weirdly. Sometimes it's good enough, but generally not.
Most games keep the collision shapes the same when animations change. Pretty much every AAA game you've ever played does this. If you really want collision shapes to change then you need to animate them physically, which is hard. You've probably played a few games like this and thought that they were not very good or had unresponsive controls.