Buteyko's Theory basically says that due to deep respiration an excessive amount of CO2 is removed from the body, resulting in a change in chemical balance which is only partially neutralized by compensatory mechanisms.
Over a period of time the loss of CO2 becomes increasingly disruptive to the functioning of the body. All physical and chemical processes are affected.
The loss of CO2, because of release from the lungs at a rate faster than its creation in the tissues leads to an increase in pH. Generally a state of oxygen deficiency also occurs due to reduction of the Bohr effect. [Less oxygen is taken from the RBC ferry.]
This oxygen shortage will cause an increase in the amount of incompletely oxidized 'products of metabolism' which act chemically to lower the pH. [Metabolic acidosis] This effect will not quite cancel out the increased pH from the CO2 loss, and the efficiency of all normal systems will be reduced.
One category of 'disease' caused by this problem may be classified as 'defense mechanisms', where the action is to reduce further CO2 loss [Asthma, emphysema, etc].
The other category are the 'diseases' which occur as a result of the changed pH and compensatory mechanisms. These include disruption of formation of fats, carbohydrates, and proteins; Disruption of the energy production efficiency [decreased ATP formation]; and a disruption in the efficiency of the processes of formation of CO2.
According to Buteyko, normalization of the breathing will not only avoid the existence of diseases of defense, but will also result in removal of the diseases occurring due to the change of function of the body caused by the excess removal of CO2. Treating the symptoms of these diseases without addressing the cause will result in eventual worsening of the problem.