So I did check and there 3 pipes, 1 for blower, 1 for incoming water and 1 for outgoing water. So, no clue there which drove me to bite the bullet and spend the $85 for a service call which he ofcourse fixed in 5 minutes. Unfortunately I was not there to see it because I'm on business travel.
The following is me paraphrasing the info I got from my wife who heard it from the pool guy. Any clarification would be appreciated so I know how to fix it next time. There is a 240V transformer that steps the voltage down to 27V in the heater. The purpose of this circuit is for safety to prevent scalding. Somewhere in that transition, there's a fuse which can lose contact over time. That fuse is no longer sold so he bypassed it. Apparently, the scalding safety circuit is not really a concern in our system (not sure how that could be). I'm not sure how this was the solution since the burners were always on (and if they're on then I assume water must be passing through and where else is it going except to the spa).