it must be enabling it back in from bikesetup once you disconnect the battery, there is no other way it can get wiped out from ECU altogether once installed from dealer.
No wrench light? Hill-hold and cruise control work? Did you press the right button and go to bike set-up and enable TSA and then go through all six gears using the clutch? This is so weird. @powernutty
I have it working again, I just had to take it back to the dealer to plug it in and reactivate my quick shifter and then go through all of the settings and put it back to where I wanted.
I have not had an issues since but I have not disconnected it either.