Hi. This is info I obtained recently when I had the same problem, and it worked for me. Hope it helps you too. The problem you now have is that the fob needs a re-synch with the car. Try this.....
MEGANE RF RESYNCHRONISING
Hold the remote control button down for longer than 10 seconds (until the red telltale
light on the key extinguishes) then press it again 3 times.
Check that the doors lock and unlock correctly.
MEGANE WITH EARLY REMOTE (LED SWITCHES OFF WHEN
HOLDING BUTTON DEPRESSED)
1. Ignition ON
2. Press and hold the central locking button for 5 seconds
3. LED on the dash board will go off, come back on and begin to flash. The flashes
correspond to the first digit of the 4 PIN security code - release the button when the
first digit has been 'flashed' and then press the button again.
4. Wait for the second digit to be 'flashed' then release and re-press the button -
continue until all digits have been entered.
5. If you have entered the code correctly the LED will then go out and the car can be
started - to code the remote, switch off the ignition and press the central locking
button again.
6. Press remote button 2 times within the immediate vicinity of the pick up (in the
roof) On some vehicles you may need to switch the ignition back on to achieve this
however.
Peejay
January 2008