Pull up/down a pin on a PCA9536 does not register?
Your I2C software must be somehow deficient, or your "short" is not strong enough to drag the pin voltage below logic "0" threshold. According to simplified block diagram for 9536 I/O ports,



the pin pad is directly connected to D input of the internal read register. So if the output is set to "1" but shorted to ground (using tweezers), the high-side transistor Q1 will be overpowered to ground, and a read from I2C register "0" should sense this. And it indeed does this, as I just verified. 

According to the PCA9536 datasheet, the high-side driver (Q1) has an impedance of about 50 Ohms (10 mA load drags the output level by 500 mV). Whether the shorting of pin driven internally to "1" is damaging the IC or not is a different question.