You didn’t state the year of your Raptor and also for In Command Issues it helps a lot if we know what version you have… such as
Pro……………………. JRVCS105
Pro Plus……………. JRVCS2
Global Connect.. NCSP3 and NCSP35
Not sure what your specific HVAC issues is with the In Command but if you haven’t then I would first try
Power down the DC … Display Commander screen
Perform a reset on the BCM
If you issue with the HVAC … and not sure what it is .. still persists then
1. Turn battery power OFF
2. Remove shore power
This removes ALL 12 volts DC up to the Zone 1 roof A/C and Zone 2, etc and allows the control modules and gateways to reset
Then turn battery disconnect back on and apply shore power and evaluate your HVAC issue
Also these folks have a pretty good support section.
https://in-command.net/control-systems/