A master key system and method for a reprogrammable lock cylinder with at least one first master pin and one second master pin. The first and second master pins have different bitting configurations. The master key system includes at least a first array of change key cuts corresponding to an input key bitting array and sequence of progression and at least two master key cuts corresponding to the input key bitting array and sequence of progression and each of the change key cuts. The system further comprises at least one master pin matrix including a master pin sequence for each change key cut and at least one rekey matrix including a rekey cut for each change key. Each master pin sequence represents a sequence of master pins configured to achieve the respective change key cut and the at least two master key cuts.