Welcome to the forum Yair
Your question contains a couple of common misconceptions:
1. The magnetic field doesn't disappear, nor does rotation of the core slow down or stop. Physical and computer models both show that it only takes small fluctuations in convection currents in the fluid outer core to change magnetic polarity. Most likely, there are several poles (four or more) during the reversal transition.
2. Pole reversals probably happen over a span of several thousand years, in which the poles (however many) migrate around the earth.
3. The magnetic field still exists during the transition.
One would suspect that migratory animals may be confused during the transition period. However, there are no indications of massive extinctions during pole reversals- so either the transition is gradual enough for animals to adapt, or they have other means of navigating.
Since the field doesn't actually disappear, solar radiation will still be deflected.
JimBob was around for the past couple of reversals- so he can relate first-hand knowledge of the process.