I'm not trying to argue, or say anybody's wrong about anything. I'm just trying to understand it myself, as an EE with a pretty fair understanding of electric motors and their typical drive circuitry.
If you ride hard, recommissioning is very important. There is a device that deals with motor position called an encoder. This can shift. You will lose or gain power from this.
Not surprised there's an encoder, in fact I'd be very surprised if there wasn't one in a modern motor. But if your encoder is actually shifting around, your problems go way beyond anything a simple tweak can fix. Very minor settling-in after initial assembly and a few heating-cooling cycles should be the ONLY drift you ever experience. There might also be some tiny drift because of the optos that read the encoder, but again, after settling in, I'd expect to see very little if any. Now sure, if your encoder phasing with the motor drive signal isn't right, you'll lose efficiency, and be down on power. But if the design is at all robust, it would have to be pretty far off to have any significant effect. Do we know how many poles the Zero motor has? I seem to recall talking about four magnets epoxied to the rotor, but my memory isn't getting any better as I get older. If it does have four poles, each is 90 degrees apart, and your synchronization would have to be off by at least a few degrees before you'd notice any loss of power at all.
I recently recommissioned a motor that would have killed the rider if he went over 110 mph. It immediately shot up to 160mph even with the kill switch hit.
Again, this may be lack of understanding on my part, and I don't mean to argue, but I have a hard time imagining how a small phasing error could cause anything like that. If the phasing isn't correct, you LOSE power, not gain it. And if things did go sideways enough for the controller to be totally confused, how could it drive the motor that hard? It relies on accurate position information to create the drive signals, and if things are totally kablooie, how's it going to do that? If things are badly out of sync, it would be driving the motor with incorrect signals, and the motor would respond something like a fibrillating heart -- a ton of random activity, with no proper power uniformly exerted in the correct direction. Finally, turning a motor OFF is simple -- stop applying power. No phase information is required to do that. The kill switch should immediately kill all power to the motor, regardless of bad sensors or anything else. Shut off the driving circuitry and no power goes to the motor. Period.
We know there's a bazillion possible ways for code to exhibit buggy behavior, which COULD easily cause things like massive un-commanded power surges and ignoring the kill switch. And sure, if you change operating parameters of the motor or if it does hit some "out of bounds" operating condition, bugs can be encountered and things could get bad. But those are firmware bugs, maybe triggered by phasing errors, but they're bugs plain and simple. Properly functioning code shouldn't behave like that, even in an error condition.
I'm not going to cast any aspersions about Zero's firmware expertise, but.....well, you know. I wouldn't be surprised if there are "magic numbers" and/or "it just works right this way" features in the firmware that don't take kindly to things like changing the RPM limit.
I know it may not make sense to you, but I have witnessed the reason to have a properly commissioned motor in person. I had never even seen this at the race track. After testing this guys stock settings with a higher max RPM I now require safety checks for every change made during tuning.
Don't shrug it off, and for the love of God, don't do it yourself
Oh, also, after recommissioning, the bike now has a top speed in the 120s and some sweet sweet regen and power.
Again, not trying to get into any arguments, and I'm not in any way trying to deny that you've seen Bad Things Happen. I'm just very skeptical that anything like that was caused by a small error in encoder phasing. I'm convinced something else is at play.