They don't actually decelerate in the Van Allen belts, though. Magnetic fields apply a force to a charged particle perpendicular to it's direction of motion. F*V = Deceleration Power = 0. Also worth noting that a charged nanomachine has a much higher mass/charge ratio than the usual charged particles (He2+, H+, and e-), so it would be much less affected.

I was actually thinking of neutralizing the seed at the muzzle to avoid troublesome charge effects.