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If it feels like the engine is missing, then thats the high temp rear cylinder cut-off. If you blip the throttle the idle should return to normal for a short time.
I was sitting in Sturgis traffic last year and I turned off the ignition. The bike next to me started to lop and I guess the rider didn't have a clue what that was. He rolled the throttle to 2k rpm and held it there. I looked at the bike behind me and said that's future work for the moco...
According to my owners manual for my 05 FXDLI there are three phases for EFI heat management.
1) Phase 1-When cyl head temp reaches approx. 320* The ECM will gradually lower rpm to 800 rpm's.
2) Phase 2- when temps reach 338*the ECM will richen the fuel to cool the combustion chamber.
3) phase 3- when temps reach 356* the fuel injection pulses are interupted thus drawing in cool air and removing heat this would be perceived as a mis-fire. The third phase occurs only when the bike is stationary.
When the speedometer senses senses motion the engine will cycle back to 1 and 2 until the cyls. cool. Hope this helps.
Engine Idle Temperature Management System. For those riders who frequently find themselves in riding conditions where the vehicle is subjected to prolonged idle conditions or traffic congestion, an optional dealer enabled engine calibration is available. This calibration offers limited rear cylinder cooling with the vehicle stopped while the engine is left at idle. This option is available for original equipment engine calibrations only. See your dealer for details.
Maybe that is why some only noticed it after the download, it might not have been enabled on it out the door.
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