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Lot of people will face a definite problem with cleanflight, even i too so i switch to openpilot which reults in better performance of flight. If you want you can reflsh the cc3d with open pilot, even after you flshed the cc3d with cleanflight
follow these simple steps
1. Load the boot loader into the cc3d FC ,you can get it here click here
2.Connect usb cable to your FC.
3.Burn the hex code.
4.Now to update firm ware, go to open pilot gui, click on update and erase the board options like.
5.Disconnect usb cable and it (open pilot) will ask you to connect the cable again.
6.Now it will load the latest firmware automatically.