@ajw22 is better versed in heater functions but I would check the Firemans switch connection. Sounds like it is closed for some reason. That is how your automation controls the heater.
 
What model heater are we talking about? Your signature just says "(with heater, 400k BTU)".
 
Not sure what’s going on but don’t you have a dedicated run for the gas line to the heater so can’t you just turn off the gas valve to the heater while on vacation and figure it out when you come back.
 
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See pages 30-32 in https://www.jandy.com/-/media/zodiac/global/downloads/h/h0574300.pdf

There are three different ways the Aqualink can control the JXI heater. You need to tell us which way it is wired to the Aqualink to discuss what is going on.
  • Remote Pool-Off-Spa Selector (3-Wire Connection)
  • AquaLink® Control System or Remote TSTAT (2-Wire Connection) aka Firemans Switch control
  • “Smart” Communication via RS-485
 

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Thank you. I’ll take a look and get back. My initial guess is the second because I have the iAquaLink 2.0 system and before this happened the display on the heater itself would read “remote tstat enabled” when in auto mode.

If that is the case then access the SERVICE SETUP MENU on the heater and see what the REMOTE is set to.

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