I assume it's remote control. (comfort control) Have you tried following procedure for selecting "Mode"?
The sail switch in the stack could be open. If it is not connected it will not recognize it. I cleaned mine with a long soft wire with a small swab of oily cotton the end. Through the exaust stack. Gently, it is in there somewhere between 20 to 30 inches. Look at the schematic of your furnace.
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