I had a problem where my key fob would not unlock my Kuga, my spare key had the same issue, I i pressed lock the lights would flash and locking could be heard. I opened the door using the manual key (great force is needed the arrangement in the key is not good), the alarm sounded but stopped when i placed the fob in the emergency location.

I attempted to start the car with the fob in my hand, notification on the dash, "no key detected" (both main key and spare). I then placed the fob in the emergency location in the center consul and started the car. I moved the car back and forth (not sure if needed), turned off the engine and everything had reset and both key fobs began to operate correctly.

I hope this is of use 

Shouldn't need reprogramming for new battery.

Do NOT buy ebay/amazon/chinese batteries

Only use ENERGIZER, PANASONIC or DURACELL, new from a reputable seller