A method and system of over the air (OTA) reprogramming of a systems of a vehicle performed by an OTA reprogramming device are provided. For example, the method includes determining whether a vehicle ignition is on or off. When the vehicle ignition is on, the method includes sending a classic controller area network (CAN) message comprising information to operate a transmission control unit (TCU), and using the classic CAN message to operate the TCU. When the vehicle ignition is off, the method includes sending a CAN flexible-data (FD) message comprising information to reprogram the TCU, and using the CAN FD message to reprogram the TCU. The method waits until an ignition of the vehicle is off to reprogram the TCU to avoid incompatibilities with a CAN FD message.