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I haven't done one of these yet. It just came out last week or so.
The technical instructions say that on some of the affected vehicles, the on-board diagnostic (OBD) system may not properly monitor the performance of the emissions control systems, which may prevent a required illumination of the "check engine" light.
The fix is just to reflash the PCM. Ford pays us .7 of an hour to do it but your dealer may need the truck longer than that due to scheduling etc.
The reflashes seem to be getting better all the time so I wouldn't worry about it causing any problems after.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.