The port on the canister - Are you sure it is connected to the main drain? Is the main drain tied into the skimmer? If you cleared the main drain from the modified cover, then it could be from somewhere else? Or is could be that the air is locked, not allowing this to happen. Only way to tell is to break the air lock (nice and slow) not to get a burst of air back in. Then try closing the main drain and repeat the process and see what happens. If you break the "air lock" and this is clearly tied to the main drain, after closing the valve, air can only travel one way and that is to the main drain. The Cyclone has enough volume for this task. If not, please call the pool company to determine how they plumb this in, and maybe upload a drawing/diagram of the sequence, etc.