Pool and Spa
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That is definitely a puzzling one...If it were me I would start by replacing the flow switch as that is the most common problem with no heat. Be sure the filters are clean or new, make sure the pumps run good and have good water pressure when running, especially the circulation pump. If you change the flow switch and it still happens, I would check to see if the circulation pump is clogged at the impeller which means you need to remove and open up the front of the pump and look at impeller for clogs.
Oh you stated it stops heating in your original question. I would still replace the flow switch as this is the most probable cause. Since the pump is good and the filter made it better, then do the flow switch
OK let me know how it goes