Why is 'Cool On' or 'Heat On' flashing on my thermostat display?
The flashing 'Cool On' or 'Heat On' message indicates that the built-in compressor protection feature is engaged. This prevents damage to the compressor by forcing it to wait a few minutes before restarting after shutdown. Wait 5 minutes for the system to restart safely, and the message will stop flashing once the safe wait time has elapsed. (Page 3)
From the official Honeywell TH5220D1029 Thermostat manual, page 3
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