He's got Micku's can on it so shouldn't it work without the Exhaust Temp Sensor? I'd pull the sensor first or call TSS. Snopro has the same pipe and no issues?
I have the same pipe on my sled, I had a couple of issues with it falling on its face when I first installed it and was going up the trail at low elevation but once I got my clutching (added pin weight and changed clickers) sorted out I haven't seen a problem since.
To the best of my knowledge the reflash is to correct an over voltage code that was showing up on some of the 12s.