Why is 'Cool On' or 'Heat On' flashing on my thermostat display?
When 'Cool On' or 'Heat On' is flashing, it means the compressor protection feature has engaged. Wait five minutes for the system to restart safely, as the built-in compressor protection forces the compressor to wait before restarting after shutdown.
From the official Honeywell T1 Pro Thermostat manual, page 2
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