The FAA examiner can examin you on every piece of equipment in the aircraft during the IR check flight. So if you're 'unlucky' enough to have an IFR certified GPS with approach capability, coupled to an auto pilot, the FAA examiner is quite within his rights to ask you to shoot an auto pilot coupled GPS approach, and more than likely during this approach he will 'fail' either the GPS or AP.This is no bad thing, it just means you need to know how to do it.
If you don't know how to use the AP or GPS its better to either remove it for the flight, or mark it as un-servicable for your check ride.
EA
