I'm in a mess....help

[Beamish]

Hello, I was carrying out some much needed rear suspension maintenance yesterday including rear arm and bottom link/Bush replacement all went ok until I came to replace the aging battery. My friend had the diagnostic port plugged in and convinced me he could fool the ECU into not resetting during the battery swap. It failed so at the moment I'm stuck with a car that starts but I have drivers window down and tailgate not fully shut and the key fob does nothing. I can't put the window up or lock/unlock the car. It seems like because of the tailgate and window positions I can't reprogram the key fob. Can anyone give me some advice? Thanks in advance. Sorry it's a 2004 e53 3.0d 218bhp.