I think they are actually referring to geomagnetic reversal, believed by some to be a likely cataclysmic event, in which the poles could reverse entirely and it is supposed that the protective field would have a dramatic reduction in power for enough time to cause serious problems.
This site is literally talking about the entire planet being forced to rotate 90 degrees due to a rogue planet passing nearby. This sudden rotation would supposedly cause the crust of the planet itself to slip and rotate due to inertia.
Well, we see evidence for magnetic reversal in the geological record. It happened before, and a lot. Also, the strength has gone down to about 5% before. This much I'd take as fact.
What is not clear is the effect this has on the biosphere. Calculations have been made for different magnetic field strenghts during the reversal and it seems that radiation can go up. By how much and how much of a problem that would be.. well. Speculations plus calculations.
The effect on the biosphere likely isn't vast. We can't see much effect in the fossil record and reversals have happened a lot.
Far more interesting--as in the case of climate change--is the effect on the economy, which is much more finely tuned and sensitive to change than the biosphere.
The hypothetical timescale of 1000-10000 years is based mostly on the low resolution of the data and the seeming implausibility of much more rapid mechanisms, but as the Wikipedia article suggests there are data that point to much higher rates.
Furthermore, the current theory is most consistent with a multi-polar field during the reversal, which would make magnetic compasses awkward, although probably not unusable. I used to sail in an area that had a large local magnetic anomaly (22 degrees over the course of a few nautical miles) and compasses weren't completely useless, just a tag tedious to use.
So if a magnetic reversal is about to occur there is likely to be a market for a "smart compass" or "compass as a service" that updates daily to your local conditions. Never a wind so ill it doesn't blow somebody good.
