The blower for the rear air has a screen that like screen in your clothes drier or the screen on your hair drier will get loaded up with lint and junk. it is a bit of a pain to access, you have to remove the right hand kick panel on the driver's side and then you could see the screen. good luck.
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Had the same problem on a 2006 pilot LX. Hot from rear heater because it comes from a separate heater core. Front heat low because ball valve faulty that controls coolant flow to heater core. The lever on the valve would move freely but the connection to the shaft of the ball valve was stripped. Ball valve may be located on the firewall under the hood. Ball valve very poor design.
If you look at your center console, you'll notice that there is an air vent on the back, facing the second row seats. This is where the rear air conditioning can be manually controlled by passengers in the rear of the Pilot...and where the air sensor is. To access it, you'd need to take apart your center console.
I had same problem. What I did was a temporary fix that needs to be repeated once in a while. Here goes. Remove the rear cup holder that is above the rear vent on the passenger side of the vehicle. Take a long Flat Head Screwdriver and try to rotate the white plastic gear clockwise by pushing it on the left side of one of the teeth. You will feel it give and should feel air coming from roof vents instead of bottom vent. It is pretty easy to do but may have to be repeated off and on.
Sounds like you need to recharge the system its probably low on r-134a. AC only works if it has enough pressure in the system. Go to the auto parts store and pick up a refill kit. If you don't know how to do it ask the parts guy to help you.