Why is 'Cool On' or 'Heat On' flashing on my thermostat display?
The flashing 'Cool On' or 'Heat On' message indicates the built-in compressor protection feature is engaged. This prevents damage by forcing the compressor to wait a few minutes before restarting after shutdown. Wait 5 minutes for the system to restart safely without damage to the compressor. (Page 5)
From the official Honeywell T4 Thermostat manual, page 5
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