I just trashed my 40mm f/2.8 Pancake trying to do the firmware update with my 5D3. I followed the instructions by the letter. The update failed and rendered the lens inoperable. Now the lens has to go back to Canon and it scared the hell out of me because I thought it might have also damaged the 5D3. Save yourself the grief I have been through today and send it back to Canon for the update.
Edit: My lens is now working again. Deleting registered batteries before doing the lens firmware update fixes the problem.