From what I understand the direction of water in a flushing toilet bowl is due to the rotation of the earth on its axis so that will not change when the earth flips its magnetic field. Actually, it has to do with the way water flows into the bowl and nothing to do with the earth's rotation, magnetic fields or anythng else.
Well, if your toilet is over 100 miles in diameter, you may get some rotation from the Coriolis effect.
For for those of us who live in the real world, you are absolutely correct.