I had the same problem when i tried to flash my cc3d with cleanflight. The problem is the boot loader is corrupted and will not load so the program you are using cannot read it. There is a program you can use to reload a usable bootloader to the cc3d. Demonstraitor GUI. You will first need to search the web for the openpilot boot loader. Not the firmwear, the boot loader. Then you will need to jump the cc3d into boot mode, open Demonstraitor GUI and load the boot loader.
Once there, you can flash the whole firmwear in openpilot to update the bootloader and firmwear. Or you can scap the cc3d and get a Naze fc for the racer so you can use cleanflight.
Where did you get the capacitor? i am missing one too. Oddly, it still flies though.