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This would be indicative of a bad sequencer in the airhandler, a bad control board in the airhandler or a bad thermostat. You say the fan continues to run even if the unit is off and the fan is set to auto at the thermostat. Is that correct?
Yesterday, after I turned off the compressor (set the thermostat to "off"), I left the fan on "auto". It continued to run for another hour or more. Now, this morning, the air handler fan is off. By the way, this issue was discussed on hvac-talk and one of the respondents said it had to do with "one thing" within the heatpump that usually works when the system is in heat mode but that it was a "head scratcher" at first. Additionally, I've read that some systems use the auxiliary heat when in defrost mode, so I was assuming the "one thing" had to do with a defrost sensor or some aspect of switch into defrost mode. Might my freon be low, the system freezing up, and the heatpump defrost being triggered?
After being off for 12 hours, I turned it back on and the aux heat came on and the outside unit was buzzing but the condenser fan did not come on. I turned it off again but the A/H fan kept blowing until I turned of the circuit breakers to both A/H and compressor. I cycled the circuit breakers to both the air handler and the compressor. I turned it back on in auto-cool and now it is working normally. What are ALL the possible causes to trip it into auxiliary heat mode? At this point it doesn't seem like there is permanent damage...