Try this sequence from my Peugeot book.
1 insert key turn on ignition then turn it off again leave key in lock.
2.turn on ignition and press the lock button on key immediately.
3. Switch off ingnition and remove the remote key from the lock and this should re-set the key and work as usual.
If it doesn't work check with Ford tech services how its done a garage billed one driver £100 to reset the onboard computer....rubbish as fare as I am concerned thats a con it's only the key that need to be re-set to the on-board computer not the otherway around.
The computer needs to recognise the key when batteries are changed.
contact for Ford UK
www.ford.co.uk send email using their online form asking how much it would cost at agent garage so you don't get stiched by a rogue garage.
Send the Vin number its on your car document to identify you are the owner they may refer you to an agent or tell you how to re-set the key if above doesn't work. repost in this as an answer to let us know how it went.
Bob UK
December 2012