I2C voltage translator PCA9306 require voltage >1V on its Vref1 pin to work properly. If this voltage is below 1V, the SCL1 and SDA1 voltages are not limited and can rise up to SCL2 / SDA2 level (5V on UniPi board). On the UniPi board, the Vref1 is connected to 3.3V from the processor board. So if you have UniPi powered while processor board is not powered, processor SCL and SDA pins can be at 5V – pretty above processor specification limits. Therefore, it is better to power up processor board before UniPi and power down UniPi before processor board.