Would you be able to provide more details around this? Are your pull-up resisters your I2C 4.7K pullup resisters enabled via a GPIO pin and you simply turn it off before any type of EN reset occurs? After reading a different Forum, I am tempted to add the hardware for this in my current PCB design. Deep Reset Tutorial
For me this would be a proactive move as I do have remote Boron but personally haven't had issues with them disconnecting. My Borons do a sleep/wake/sleep cycle and routinely connect/disconnect themselves from the cloud due to being battery powered but was tempted to add this type of hardware. I'd like to make sure I'm preventing a possible future problem vs injecting a new problem as you experienced. In my design, all sensors are turned on for 50-250 ms or so to take sensor readings and then turned off before falling back asleep. Given the info here, I assume I shouldn't have any risk of back feeding power to the boron but not sure if I understand it fully yet. Any guidance or further details would be appreciated!