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The Crazyflie 2.0 contains two micro-controllers (nRF51, STM32F4) and upgrading/flashing can be done in several ways.
The Crazyflie 2.0 contains a bootloader with which it can be used to updated both micro-controllers over the air (OTA). Either using the cfclient or from command line.
This is mainly for development and requires a JTAG debugger and an adapter to the Crazyflie 2.0 connector.