The article doesn't say how long the polar flip took on the sun, and I have no idea how long it would take on earth, but if it happend quickly (say, less than an hour), I'd sure hate to be airborne when it happened. Virtually all aircraft still depend on magnetic heading indicators for primary navigation. Not a compass per se (although all U.S. aircraft are required to have a compass), but usually a flux gate that drives the primary heading indicator. Sure, some of the ultra-recent aircraft do display a heading from GPS, but even they have some sort of magnetic heading indicator. I think the initial reaction would be to assume the GPS signal is faulty since most people think of the earth's magnetic field as a constant. As a pilot, it would be very confusing to try to sort out while airborne, especially since the compass is one of the few things that's "always right".
Worse, most of the U.S. aircraft fleet (as in, all the small stuff, it vastly outnumbers the big stuff) is entirely dependent on magnetic navigation. You usually set the directional gyro manually, then periodically recheck it. But if you looked up and saw a big discrepancy between the gyro and the compass, you'd assume the gyro was about to die, since that is a primary failure mode of gyros. You'd presume it was dead and start navigating off the compass.
Now you've got all these airplanes going all over the place, everyone confused because things aren't matching up at all, ATC yelling at airplanes because the headings they're flying aren't what ATC wants. At some point, virtually every aircraft starts declaring an emergency because their navigation equipment isn't working right. It would be a huge mess, that I think we'd be lucky to not have large scale loss of life as a result.
So much for the alarmist point of view. If it happened fairly slowly (say, less than 5 degrees per hour), pilots could compensate until the scientific community got the word out, and ATC was informed so they could broadcast it. You'd still end up with a few people in small airplanes getting very lost because they hadn't heard about it, or weren't talking to ATC. It's still possible to fly in a lot of the U.S. with no electrical system (and therefore no radio). But loss of life would be minimal or none, since all of the aircraft that weren't in contact with ATC would be in visual conditions, and probably flying somewhat by landmarks anyways.
Why did I flip? I got tired of coming up with last minute desparate solutions to impossible problems created by other fucking people.
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