I am not sure if I mentioned it a little in my journal a while ago, where I also realized that I looked a little different in photos. If I recall correctly, Jhanananda said something about the muscles of the face since we tend to relax.
I learnt in medicine that any living tissue (bones/muscles/ligaments/tendons) is subject to changes according to how subjected they are to stress. So it could make sense that when we are less stressed, certain muscles are less or more in use - perhaps more blood-flow to areas like the scalp could aid a change in skull shape. For example, more brain usage in certain places create enlargements/more synaptic connections (they call it neuroplasticity). Astronauts do not have gravitational force acting on them in space, so they tend to hollow out their bones and get osteoporosis.
On a personal note, my face also became more squarish. I suspect this has to do with my tongue pressure on the palate, pushing up the maxilla (front part of the face), which is antagonistic (opposite action) to the jaw-clenching muscles. This would tend force the jaw to rotate forward. My shoulder posture improved as well. Due to awareness of my body's pain, I've continuously adjusted and done some postural exercises, so it looks a little different from the side as well.
I've heard of some accounts where some cultivators seemed to experience rushes of energy(viriya?) resulting in cracking noises of bones. I have only heard of them and hence take them with a pinch of salt. They seem to be often related to kundalini. I have heard of it as "purification of the earth element" in some yoga schools, where the bones and muscles of the body are taken to be the earth element.
