Assuming the new battery isn't also flat - you could swap it for another to be certain - you can try resetting the warning. Start the car with the affected key fob, then press the lock and unlock buttons once, which forces the car to recheck the fob battery level. If this is unsuccessful it may be that there is an issue with the fob itself, If you don't have a spare, you may need to try an automotive locksmith or independent Ford specialist who can check the operation of the system.