What happens when the North and South poles flip?
First of all I will try to explain what a geomagnetic pole reversal is.

A magnetic pole reversal happens when the magnetic field weakens until it can no longer sustain itself. This can take 1000-3000 Years or more to complete the time it takes is very variable.

After years with a weak and sometimes variable magnetic field. The magnetic field re emerges in its original, or in a changed direction. So it is not the poles moving over the surface of earth.

Link https://en.wikipedia.org/wiki/Geomagnetic_reversal 

What happens during a geomagnetic pole reversal.

During a pole reversal earths magnetic field is weak so our planet is less protected from cosmic radiation and from the solar wind.

Link https://en.wikipedia.org/wiki/Earth%27s_magnetic_field

This increase in cosmic radiation does not fit any of the known extinction events that have happened in Earth's history. This does not mean nothing at all will happen to life during this time it only means the dangers are low.

If you want to follow how the cosmic radiation changes you can do this on the last part of this page http://spaceweather.com/ 

Link https://en.wikipedia.org/wiki/Cosmic_ray

I mentioned in my comment Earth's magnetic north pole is really in the south. To understand how this can be true in a magnetic compass the magnetic north pole is repelled by Earth's north pole so it does point in the opposite direction (a bad explanation but it is how it works).