I'm assuming that reading the configuration EEPROM is one of the last things the SoC does, so if we see activity on the I2C bus, this would suggest that the SoC is alive and has POST-ed.
If you disable the EEPROM or remove it, the SoC should register an error condition. If there is any visual indication, eg a flashing LED, and if this differs from before, then we could assume that the EEPROM is OK.