Assuming we could shelter everyone, and design farming machinery to shield the operators so we could continue to grow food from our shelters, there is still a very large question of what happens to the eco-system during this time. Lots of additional radiation will be reaching the earth's surface and we can't protect all of it. Maybe the mystery of how evolution seems to run in 'fits and starts' will be answered when the magnetic field winks out for a few centuries during its flip...
