When a punch at the end of a fully extended arm comes to a sharp stop, it is because it cannot go any further, and, as it stops, it pulls the elbow and shoulder joints apart. When a punch is focused to stop before full extension, everything comes to a smooth stop. When a punch is focused, it may be stopped short of the surface, on the surface, or beyond the surface. Either way, if the punch does make contact with the target, the arm and body are able to absorb the reactive force. If the arm is fully extended, it cannot be adjusted to focus the stopping point and, if it makes hard contact, the elbow may be injured.
As you train, you train your body to make movements to accomplish your purpose. If you lock your punches when you train, your body makes adjustments to try to accommodate for the movement. If you try to punch hard with a locked out elbow, the body will may changes to its movements in an effort to protect itself, usually by limiting the force it applies to the punch. When you change the way you punch and do not lock the elbow, the body keeps using the movements you have trained it to do in the past, and the punch feels awkward and less powerful, which may be true. Once you have trained for a period while punching correctly, the body will adjust itself to the new movements and the punches will be just as, if not more, powerful than before, and you will not be stressing your joints.