It appears the small sample size I looked at gave me the wrong idea. The profile FCND_Menu.cueprofile just had the F/R turned of, but now that I have looked at more profiles in the Far Cry New Dawn SDK-folder most of them just have nothing in their Lighting Channel.
I could swear that I looked at FCNC_Day and FCNC_Night as well yesterday and that they hade the Front/Rear issue, but both of those also have empty Lighting Channels now.
The first two profiles I looked at today (FC_Takedown and SDKL_Alarm) both had partial LEDs selected, the first 96 LEDs from the top left, eding in the Rear side of the 3rd fan. All profiles I have opened after that are blank. I'm starting to feel like iCue are changing and adapting to my efforts as I go :D
EDIT: OK, something fishy is going on! I am 100% sure that yesterday I looked at and fixed the profile FC_Benchmark, since it was an easy profile to check if it worked. It had the problem with Front/Rear not on, and I changed that. Today the Lighting Channel if that same profile is empty... WHAT is going on?!