Indeed, it will go through the filters of the airdog, whether it is running or not.
My airdog II motor died after 20k miles... Fuel leaked along the axle of the rotor and locked the electrical connectors inside.
Disassembled it and cleaned it out, replaced filters (prefilled the water separator) and now it is running again.
I noticed the problem by the lack of the sound of a running airdog (duh) and slower throttle response.
Now I tilt the AD a bit so if it leaks again along the motor axle, the fuel would leak at the front instead of
contaminating the rear of the motor where the contacts are...