Most cars require the fob to be synchronised with the immobiliser when the battery has been changed. Have a a look in the manual for the car, as this process varies from vehicle to vehicle.
this happened to me where the car wouldn't start. I called the RAC, and he kept opening the door repeatedly with the key (central locking), until the immobiliser somehow synchronised itself and stopped flashing.....car started. This may have been a fluke though!