At the risk of providing mis-information, I think I would need a little more information or a schematic that shows the system arrangement to help answer the question. Some questions or clarifications in lieu of this:
- I'm assuming your system is all electric.
- You are using your boil kettle as a heat source during mash, so it's like a traditional Hot Liquor Tank.
- You say water being circulated while auto-tuning. I'm assuming this means you won't actually be brewing, but using water instead of wort.
- The Boil Kettle contains a water heating element that is controlled by, call it, PID#1 and has a related sensor, (call it sensor #1) in the boil kettle water. You have a pump that moves the water around in the Boil kettle and past sensor #1. Please confirm.
- During Mash, your wort (or plain water during the tuning) would be pumped out of the Mash Tun, past a sensor (call it sensor #2) into a coil submerged in the Boil Kettle which also contains separate plain water. The wort then returns back into the Mash Tun.
- Sensor #2 is connected to PID#2.
Questions: What does PID#2 control / what is it commanding?
Initial guess is that PID#2 is not really needed during mash, unless it is trying to control something. You can just watch the temperature it displays and that is the best indicator of live mash temp. PID #1 will control the boil kettle water (being used as a HLT) to your mash setpoint on PID #1 and with some slight lag, the mash temp in the mash tun will follow it closely. Auto-tuning PID#1 with this arrangement should work fine.
I hope I'm getting this right without a schematic. Every system is a little different.