A method for controlling a heat engine system, comprising: initiating flow of a working fluid through a working fluid circuit having a high pressure side and a low pressure side by controlling a pump to pressurize and circulate the working fluid through the working fluid circuit; determining a configuration of the working fluid circuit by determining which of a plurality of waste heat exchangers and which of a plurality of recuperators to position in the high pressure side of the working fluid circuit; determining, based on the determined configuration of the working fluid circuit, which of a plurality of valves to position in a closed position to isolate a portion of the working fluid from the working fluid flowing through the working fluid circuit; receiving data corresponding to a measured temperature and/or pressure of the working fluid flowing through the working fluid circuit; determining whether the measured temperature and/or pressure exceeds a predetermined threshold; and actuating, if the measured temperature and/or pressure exceeds the predetermined threshold, one or more of the plurality of valves positioned in the closed position to position the one or more of the plurality of valves in an opened position or a partially opened position to enable at least a portion of the isolated portion of the working fluid to flow through the working fluid circuit.