My best understanding is that motor commissioning is the tuning of the Sevcon controller sine wave programming against the motor position sensors so that the field is applied correctly.
This would reduce wear on the motor bearing and minimize wasted current.
I've added a provisional manual section for reference. I'd referred to this before as "controller alignment", but I realize that the proprietary term gets thrown around and deserves an index entry...
http://zeromanual.com/index.php/Unofficial_Service_Manual#Motor_Commissioning
That sounds like a reasonable thing to do if there has been any factory experience with the sine wave programming wandering. However, I do find the term "commissioning" kind of goofy and rather obtuse.
I continue to believe, based upon many years of riding and owning motorcycles, if everything is working just fine and you are happy with your bike's performance, don't mess with anything. It will likely get worse.
Mostly, I agree, and I try not to mess with my bike at all until/unless strictly necessary.
However, part of my nuclear technician background disagrees: I spent a good part of it helping run a program where we'd attach 6-axis accelerometers to sensing points on equipment, to study motor and bearing wear and predict problems. It was clear that anticipating a wear problem by observing non-concentric forces on a shaft or axis was worth the time invested, and our plant's defect rate dropped considerably.
I think motor commissioning falls into that category, and the Sevcon DVT software does make this relatively straightforward, so I think Zero's recommendations here are appropriate: once 600 miles after getting it on the road, and then yearly or every 8k miles.
Sure, there's probably some slack in the interval, but I wouldn't let it go. Again, the point of maintenance is to catch problems before they cause damage, and the imperceptible problems are the ones to mind carefully.
(Also, I see that Sevcon refers to this in their manual as "controller commissioning" which is a little less awkward a term).