Updating betaflight with a CC3D can be stressful if you don't take the proper steps. Here are the steps I take to do it successfully.
EDIT: (2-15-2016) - I believe Cleanflight firmware stopped supporting flashing from Open Pilot. You can still do it with betaflight CC3D_OPBL but I recommend checking out http://www.southquay3d.com/index.php?route=news/article&news_id=9 for a more permanent solution.
EDIT 2 : (4-14-2015) - Since using the non-OPBL way to flash my CC3d I have not been able to flash anything else even attempting to connect to it with my FTDI adapter. I found it easy the first time but haven't been successful since. Because of this I recommend sticking with betaflight C3D_OPBL and even though it's a painful process it's not all that bad.
1) Open OpenPilot GCS
2) Plug USB cable into CC3D but NOT the computer
3) Click the Firmware Tab in OpenPilot
4) Click Upgrade & Erase
5) It will ask you to plug in your board so do so.
6) It will upgrade and erase then connect and start the flight time counter.
7) Click Rescue
8) Disconnect and reconnect USB
9) Click open and browse to betaflight_CC3D.bin on your local machine.
10) Check I know what I'm doing and click Flash. It will go pretty quick and you'll see blue led on your CC3D blinking. After it's done wait 20 or so seconds.
11) Disconnect USB
12) Open Cleanflight configurator
13) Plug in Battery
14) Plug in USB after the beeps
15) Cleanflight should pick up the com port. Click connect
All done! Change some settings!
Whenever you click save and reboot it will disconnect from Cleanflight config. Just wait a few seconds, disconnect the usb, and reconnect. Sometimes I have to close cleanflight and open it again for a proper connection (With the newest configurator it seems like I hvae to do this more often). Other times I have to disconnect the battery and usb then reconnect.
Download betaflight from https://github.com/borisbstyle/betaflight
The cleanflight configurator is a chrome extension so add it through chrome.
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