There has been evidence found of physical equator shift in the earths history. There have been theories that when the earths magnetic poles flipped (not shifted) that the earth “tumbled” until it regained equilibrium. Regardless, as you said, if that happened the space elevator would be the least of our problems.
The magnetic poles have nothing to do with the Earths rotation. The magnetic North Pole is not even at the “true” North Pole. (Where Santa Claus lives. ;~)). Magnetic north is somewhere in Northern Canada now but it does move and could even flip as you said. But it would mean nothing for the rotation of the earth or where true north and south are or where the equator is.