At boiling temperatures, the pump will not work, not because there is anything wrong with the pump but because the wort vaporises in the pump due to it continuing to boil. This creates cavitation in the pump which results in it not pumping the liquid well.
Once the boil has finished and heat is not being actively applied to the wort, the wort will rapidly cool down enough to start pumping. As soon as the temperature probe is reading 99/98°C (208/210°F), the pump will work.
As a precaution, before your next brew, open the bottom of the unit and double-check the connection of the pump to the control box. If it is a little loose, it may work fine at lower temperatures but after a sustained boil the connection might be too loose to work properly.
What will keep the pump from starting while boiling?
The conical shape of the bottom of the boiler and the sizeable conical heating element provide more significant heat transfer and distribution to the wort during the boil. However, as a result, when hot wort is drawn over the element as it goes to the pump it retains heat and boils in the tube leading to the pump. This can cause an air cavity in the pump, resulting in the pump not starting. This only occurs while the wort is boiling, and the heating element is on. Turning off the element and restarting the pump will get the pump going again.
For the above reason, when sanitising the Counterflow Wort Chiller, we recommend you do so at the end of the boil without active heat from the boiler. Temperatures above 85°C (185°F) are considered to sanitise surfaces. Therefore, running the pump for 1-2 minutes, post boil will achieve the same result as during the boil.