Or maybe there's a Primary-throttle position sensor (the one that people refer to as the TPS when it plays up).......
...... and a Secondary-throttle position sensor as well..... unrelated to each other.
If you physically remove the Secondary-throttle butterflies and leave that sensor & its stepper motor alone, it just continues to go through its normal motions but doesn't know that all that the stepper motor is turning are the shafts which USED to have butterflies on them. You won't get an error code cos it thinks it's doing the right thing. .... as long as you do NOT disconnect it.....
Leigh.... that is UNLESS the secondary throttle sensor is crook, in which case it will of course throw an error code no matter what. The only way out of that is to either re-set/replace it, or modify your ECU tune to disregard that particular error code (best of luck with that last bit!). I don't think there will be any operational problem, but you'll get sick of looking at that lil' idiot light ....