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 upstream of a first expander and a low pressure side downstream of the first expander by controlling a pump to pressurize and circulate the working fluid through the working fluid circuit; determining a configuration of the working fluid circuit based on data received from one or more process condition sensors by determining which of a plurality of waste heat exchangers (102a-d) to position in the high pressure side upstream of the first expander and which of a plurality of recuperators (130a-c) to position in the high pressure side upstream of the first expander and in the low pressure side downstream of the first expander; determining, based on the determined configuration of the working fluid circuit, which of a plurality of valves (116a-d, 118a-d, 128a-d) 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 (116a-d, 118a-d, 128a-d) positioned in the closed position to position the one or more of the plurality of valves (116a-d, 118a-d, 128a-d) 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. initiating flow of a working fluid through a working fluid circuit having a high pressure side upstream of a first expander and a low pressure side downstream of the first expander by controlling a pump to pressurize and circulate the working fluid through the working fluid circuit; determining a configuration of the working fluid circuit based on data received from one or more process condition sensors by determining which of a plurality of waste heat exchangers (102a-d) to position in the high pressure side upstream of the first expander and which of a plurality of recuperators (130a-c) to position in the high pressure side upstream of the first expander and in the low pressure side downstream of the first expander; determining, based on the determined configuration of the working fluid circuit, which of a plurality of valves (116a-d, 118a-d, 128a-d) 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 (116a-d, 118a-d, 128a-d) positioned in the closed position to position the one or more of the plurality of valves (116a-d, 118a-d, 128a-d) 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.