What does the compressor protection feature do?

The built-in compressor protection feature prevents damage by forcing the compressor to wait a few minutes before restarting after shutdown. During the wait time, the display will flash the message Cool On (or Heat On for heat pumps). When the safe restart time has elapsed, the message stops flashing and the compressor turns on. Wait 5 minutes for the system to restart safely.

From the official Honeywell TH6220D1028 Thermostat manual, page 15

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