Why would woman accustomed to wearing high heels experience discomfort when wearing low heels?

Tendon tightness. High heels alter a person's gait along with changing the stress placed through the foot. Chronic high heel wearing can lead to tightening(shortening) of the calf muscles/tendons over time. Going to a flatter shoe can then lead to these tightened structures becoming irritated or shifting stress to other foot structures causing pain or irritation. Dr l.
Law of Davis. When the soft tissue of the body (ie the achilles tendon) is placed in a certain position for prolonged periods of time the body will accommodate this position. In the case of the achilles tendon, when in a shortened position from shoes with high heels, after time the tendon will become resistant to stretching and cause pain especially where the tendon attaches to the heel bone.