When an animal has a negative experience, he will use any new information he associates with this event to form specific beliefs, thoughts and feelings about himself, his world and the people and animals around him.
This is an instinctive survival response in all animals, including humans. If it didn't happen, we would never remember not to touch a hot kettle after burning ourselves on it the first time.
However, when a negative experience has been overwhelming, the stored information can include strong emotions, feelings and urges, which are then triggered every time any aspect of the original event is re-experienced.
In AIT, cognitive behavioural therapy is about looking at the animal's learned, negative thoughts, emotions and behaviours as a connected whole, and helping him to recognise them and change them to more positive ones. Usually, once an animal realises that it is just his learned thoughts and feelings that are making him feel bad, he is keen to be helped to replace them.
In practice, I find CBT works better alongside other psychotherapeutic techniques (such as regression and EMDR), because while CBT works at the conscious, rational level, it is more effective when the underlying (and often unconscious) memories and associated trauma have been resolved and released.
Photo Carriage Horses (c) Silva Dymakova