The invention is directed to methods of shutting down reaction systems. The reaction systems are those that use catalysts that comprise molecular sieves, particularly metalloaluminophosphate molecular sieves, especially metalloaluminophosphate molecular sieves which are susceptible to loss of catalytic activity due to contact with water molecules. The methods provide appropriate mechanisms of stopping feed to the reactor and unloading catalyst to protect against loss of catalytic activity that can occur due to contact with water molecules.