Low end sputter, hesitation

[HikerToo_imp]

If your CB has an actual problem, sending an ECU "out" is not going to "fix" a problem. And also, sending an ECU without having the CB on his Dyno is just guess work, that is why last year, Don needed a CB to tweak the ECU while IN the CB and ON the Dyno. I brought mine in and he did that, it helped overall performance, I still had the hesitation you seem to be describing, I was lucky, mine was fixed by the throttle trick. My CB has the Staintune while on Dyno.
The ECU flash Don is doing, based on having my CB in his shop did the following.
Air/Fuel mixture - slightly richer, probably close to the default PCV map available on their website
Timing - Advanced in most lower gears
RPM/Throttle limiter raised or removed.
He did my Dyno with pair valve in place, like OEM
I never did block my pair valve again because it runs OK with it in and I did not like the gas fumes when blocked.
So, you may have a problem, the ECU flash is not causing it , but will not fix it either. If you have a good running CB to start, the ECU flash will improve performance, if you want custom ECU tweaks due to other mods, they would just be guessing without having your bike too.