FC is Filght Controller mounted on the quad. There's a cable(s) that plug into the Rx Receiver and four sets of wires that plug into the ESCs which control the motors.
I'm not 1000% sure that it prompts to remove USB but I'm 96% sure that it needs to be power cycled after upgrade.
If you still have problems the exact make/model of the quad would help, and/or pics of the various components.