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, apps or from command line.

• Upgrading using the cfclient
• Command line. Convenient for developers. This is also available as a make target in Eclipse in the VM.

• Video tutorial for Crazyflie 2.0
  

Got to the upgrade tab in the settings menu of the app and follow the instructions.

Only the STM32F4 MCU can be flashed using dfu. Please see these instructions on how to do it.

This is mainly for development and requires a JTAG debugger and an adapter to the Crazyflie 2.0 connector.