Viper two way remote problem

Hi, I have Viper 5901 alarm installed several years ago. Recently my two way remote got completely discharged and when I changed it back - it does not talk to the car anymore. When I press a button (say lock) a transmit icon is displayed for a fraction of a second, but nothing happens to the car. The second small remote works fine so I assume the problem is with the remote and not with the alarm. I let the battery totally discharge many times but it always worked properly after charging. Now it doesn't. What could it be? 2.I tried to pair the remote and here is another question. The instructions say open the door, turn the ignition, then press valet button and release and then press it until the LED flashes. I am pressing the button but the light never goes on. When I use the second remote to lock the car - the LED flashes and car locks. What I am doing wrong when trying to pair the remote so that the light never flashes? Thanks.