A magnetic reversal dosent completely cancel out the Earths field. All the reversal does is have the dipole field go away and then come back reversed. The quadropole and octopole moments will still remain.

All this is a bit irrelevant to the OP tho. Basically, even if the Earth completely lost its magnetic field, all that it would do to the atmosphereic loss rate would change it from almost zero to very slightly more than almost zero.