A system includes a cylinder event module that determines an air-per-cylinder value for a cylinder intake event or a cylinder non-intake event of a current cylinder based on a mass air flow signal and an engine speed signal. A status module generates a status signal indicating whether the current cylinder is activated. A deactivation module, based on the status signal, determines a current accumulated air mass in an intake manifold of an engine: for air received by the intake manifold since a last cylinder intake event of an activated cylinder and prior to one or more consecutive cylinder non-intake events of one or more deactivated cylinders; and based on a previous accumulated air mass in the intake manifold and the air-per-cylinder value. An activation module, based on the status signal, determines an air mass value for the current cylinder based on the air-per-cylinder value and the current accumulated air mass.