You can run the same code (firmware) on both the trueHWIL sensorless autopilot and the autopilot in your UAV. The trueHWIL autopilot cannot be used in a real UAV (as it is sensorless) so you will need another autopilot to go into the UAV. You can take the gains, mixing, and other settings (configuration file) from your trueHWIL sensorless autopilot and use them on the autopilot in your UAV.
In summary, the same settings and autopilot code can be used on the flying autopilot as was used in the trueHWIL simulations. As long as your aircraft model is accurate, the settings will be correct and the gains should be close to what the real aircraft needs.