Exemplary embodiments are directed to a system and method for configuring a control device in an automation system. The system including a hardware structure, and a programming tool connected to the hardware structure and the control device. The programming tool is configured to transmit a control program and configuration files to the control device, and store a control project in memory. The programming tool registers modifications of the hardware devices using software “FlexConf.ini” as modification information and sets the control device to a mode “control with flexible configuration” via a parameter “FlexControl”. The programming tool also determines a type for transmitting the modification information in the parameter “FlexControl”, and transmits the modification software with the modification information stored therein in accordance with the transmission type set in the parameter “FlexControl” to the control device. The control device then parameterizes the hardware devices and transitions into a “RUN” operating mode.