@Paulv it sounds like they remove the cem module from the car, and have the equipment to read out the key/ pin code directly from it for programming.
Re: aircon
If passenger side is cool and driver's side is warm it usually indicates it low on refrigerant but a common issue on the 6cylinders is the suction control valve on the A/C compressor (diagnosed via A/C pressure gauges)
If it's only occured after the key programming you may just need to have the climate control calibrated by someone with VIDA