To sync your remote with central lock there is two ways. One you close car by key and in 1 sec press unlock button and it should work. If not second way is to clear memory and reprogramme all remotes. To clear memory in central lock put one of your keys in ignition and turn it to position on but don't start engine. After that get out of your car and with second key close your car (not with remote) and press 5x unlock button on your remote. The indicators supposed flash each time U press unlock. Next step open your car with key and take it out the other one and close car by key. Wait about 1 min and open car put one of keys in ignition and turn it to on.(Take it the fob from remote from key in ignition). Close all windows and close door by key and press on your first remote one time unlock and indicator supposed flash one time wait 15 sec and press and hold unlock for confirmation and car should open. Next step take key form ignition and test unlock and lock.
Do the same for other remote but when U will program it U have to press twice unlock and again wait 15 sec and press one more time unlock to confirm.
Source:
http://www.vwaudiforum.co.uk/forum/showthread.php/86888-Audi-A3-Key-Fob-not-working-!