If you don't want to/can't use the Reboot Controller VI, then there is no direct way to do this that I know of. The RT can restart as soon as it is reset if you have a start-up exe on the controller. To my knowledge, the FPGA cannot automatically reset itself however. This is why I suggested to put your entire FPGA code into a loop so that it can effectively reset itself by looping back to the beginning of the code as soon as it resets the RT. Hope this helps.
