Update: 10-23-2024
After tabling this issue for the past couple of months, we had to revisit it when we performed a major upgrade to our system that caused the issue to come back in full force to the point where our "automatic" workaround (basically, detection of the issue and software reset) wouldn't work anymore.
We replaced a lot of our 24V hardware with new versions of the same devices and went to different, dual 24V power supplies as well.
After the upgrade, we ran into the disconnection issue almost immediately when trying to run the equipment. We would get tens, almost hundreds of TfrRdy pin glitches in matter of seconds and the Pi/Duet would disconnect within 30s. We disconnected one 24V device at a time and ran some tests until we found that a brushed 24V/2A vacuum pump was putting out excessive noise on the 24V wire which was feeding back to the Pi/Duet. We put a capacitor across the pump's terminals and the TfrRdy pin glitches went to 0. We've been running for a couple of days now and we haven't had a single disconnection between the Pi and Duet.
It looks like our problem was excessive noise generated by poor component selection/sourcing. We tested the other pumps and devices on the system and we are seeing varying amounts of noise but none to the extent of that one particular vacuum pump.
I'll mark this one as solved!