First off, the north and south poles don't even have the polarities right now, if you use a compass, the north pole actually points to an area in Canada, may be another country around that latitude. The change is always in progress though. Also, the only way that it might directly kill you is if you were in a life and death situation and you were on the spot where the north or south magnetic poles are at the time, making it useless, lol. The Effects of this aren't going to be felt by anyone in their lifetime unless they live to be about 1,000 years old. Old enough to see a change. What actually changes, however, are the magnetic poles. What your compass points to. The gravitational poles are there to stay and, as far as I know, never change. So the orbit around the sun, just like the rest of its 4.5 billion year journey through our 13.7(or so) billion year old universe, is not going to change due to the magnetic poles switching.
And, secondly, this change is much to slow for it to be felt by, or for it to effect wildlife who use the poles for navigation. Planes, ships, and electronis devices will not crash or be useless during this period (at least not because of it) because they all work fine right now, and as i said, it's constantly shifting. You were right that it will take around 400,000 years as far as I know, but it may be longer. It, however, is not going to take mere hundreds of years.