My dear 2013 C-Max SE nuked me with a battery failure Tuesday, March 17, 2015. (VIN 1FADP5AU0DL511701, odometer 16,859 miles). This was 14 months and ~10 K miles since the last time it happened and at that time it was "fixed" by "re-flashing the FCDIM 13B12B". That was January 1014 after peculiar behavior and failing the second time in a week or so. Basically had zero voltage available. No reaction to/by anything electrical. Using a battery charger I had found that the battery seemed to recharge surprisingly quickly. I had discovered that the emergency fix was easy.
Here's the story. Nothing wrong with the battery, the problem is in a control module (that had been re-flashed) it cuts off the 12 V supply to everything. Hooking up a battery charger or jump-start battery isn't recharging a bad battery. The control module is reactivated by briefly exposing it to 12- 14 V, a minute or so or maybe just for a few seconds and whamo, everything is back to normal. So I did that again and it is going on a week now and everything is completely normal.
So there, folks. See if this works for you if/when needed and let us hear about it.
The next day, with my perfectly running C-Max, I went to my nearby Ford dealership and their service people checked out the battery system. "Performed 3 battery tests, all passed. Performed ECC tests, passed. No codes present. Uploaded to Ford. Will contact customer if Ford so advises". It looks like they got into the high voltage as well as the 12 volt system. They did not re-flash anything this time.
I have just noticed in the latest Consumer Reports auto issue, the C-Max hybrid is rated unreliable in things electrical whereas the Fusion hybrid, after the first year looks very good. I mentioned this to the service foreman and he said they are not the same system at all. I thought they were the same.