Hi Andy
The purpose of the secondary throttles is primaraly to smooth out airflow to stop bogging then surging when the throttle is opened sharply, and to generally give a smoother power delivery.
They are also used to reduce power under certain circumstances, such as traction control operation or gearchanging.
On the 1400s the secondary throttle shaft also has a cam on one end which can open the main throttle and is used as a fast idle device for cold starts.
I know that owners of the early bikes removed them as the 2006 model had their operation set to make power delivery smooth and docile below 5000 rpm.
Removing the secondary throttle can lead to a coarser power delivery and less driveability.
Hope this helps.
Regards
Steve Haswell
KMUK Customer Service