I've had my car for 10 years and have never drained the water separator because the drain broke off and was plugged with some kind of gas tank repair stuff. Is it really that important? I have another one that's not broken and have been thinking about changing it.
I'd leave it alone. If it starts to leak, then you get air leaking in, your pump will not be able to draw fuel from the tank. I have bypassed mine on an old Jetta that I was using until recently. The plastic had gone quite brittle developing a steady leak. Just chase the water with an additive now and then plus change the under hood fuel filter every fall.