Yes, you need to reprogramme after battery replacement.
1. Obtain a remote (can be a second hand one - they can all be reprogrammed, or you can buy a new one for about $90 from Ford).
2. Close the doors.
3. Turn the ignition key to the accesories position.
4. Within 5 seconds of turning the key, hit the rear demister button (center console) three times in succession.
5. The door locks will cycle once to indicate the special mode has been entered.
6. Press any button on the remote you wish to program.
7. The doors will cycle to indicate a new remote has been programmed.
8. Continue steps 6 and 7 for all remotes (including existing ones) you intend to use on the vehicle.
9. When you’ve programmed all the remotes, turn the ignition key off. The doors should cycle again to indicate the programming session has been completed.
It’s interesting to note that you are not actually programming the remote per se, but rather you are programming the car. The late model Ford’s all have a BEM (Body Electronics Module) which is basically a fully fledged computer. When you press the remote, it ’squawks’ a unique code to the car BEM. If the BEM is in the special programming mode, it then enters this code into memory as an authorised fob.