Thank you guys for confirming that. I knew you couldn't just ignore the body diode.
No there is no level shifting going on. It's a 3.3v circuit. I've made a model of what the current state of it is.
Now based on the maximum forward current my hunch is
we fried Q1 and Q3 when the second i2c master used to be connectedWhere the red text second
SCL/SDA master is there was another set of fets (same part facing the same direction toward the eeprom) and we tried to drive the eeprom from the controller on the board with it's built in i2c engine. This is the same controller driving the Enable signal. The processor is driving a 3.3v output just fine. The idea is that the processor will enable the vpd which will disable the vpd bus from an external host. They tried to do isolation with a few fets but when I looked at the circuit I saw this, which I know isn't true isolation because of that body diode.
I believe this was put on the board because they thought the processor didn't support multimaster i2c. Which it said in the first line of the data sheet description of the i2c controller.
We'll probably end up ripping this out but here's the weird behavior I'm seeing.
At this point the second master is disconnected. I've also disconnected the SCL and SDA signals on the left side. So the only things on the circuit are the processor enable gpio output, the pull up resistors, and the eeprom.
When the Enable signal is sitting at 0 everything seems fine. SCL and SCL EEPROM are sitting at 3.3v. But when Enable is driven to 3.3v, SCL drops to approximately 0.7v and SCL EEPROM drops to 0.1v. I see the exact same behavior on SDA
I don't see where all the voltage is going unless Q1/Q3 was somehow fried by pushing 3.3v across the body diode and the voltages are escaping through the gates to GND.
EDIT:
So I forgot about the maximum prospective short-circuit current.
https://en.wikipedia.org/wiki/Prospective_short-circuit_current The default supply drive strength from the processor is only 8mA and the pull ups would limit the current too. So I don't think anything could get into the circuit with enough current to short it out. So now I'm really stumped