Only if they are shot in a vacuum. When you factor in wind resistance, the 350 grain arrow will slow down much faster than the 600 grn arrow, simply because it doesn't have nearly the energy or momentum to fight thru the wind resistance like the 600 grn arrow does.
ArthurP,
If the 350 gr arrow is a smaller projectile, which is most likely the case, then wouldn't the smaller projectile have less draw and a smaller coefficient of friction? That would offset the difference in momentum?