A method and system for modifying the function of a state machine having a programmable logic device. The method including: (a) modifying a high-level design of the state machine to obtain a modified high-level design of the state machine with a modified function; (b) generating a programmable logic device netlist from differences in the high-level design and the modified design; and (c) installing the modified function into the state machine by programming the programmable logic device based on the programmable logic device netlist.