Research for hypnotherapy is relatively easy with brain scans; they have no ill effects and can be used to see inside the brain at the moment of hypnotic suggestions. The research seems to show that the parts of the brain which decide what to concentrate on, selectively down regulates. That means that other thoughts are less focused on and the suggestion you want is given more attention. The confidence we have is because we know that for many conditions hypnotherapy works.
Evidence-based practice includes mainstream psychological and health research in the use of clinical hypnosis. In other words in cannot be true hypnotically and untrue medically, facts are the basis for opinions, not the other way round.