Those fragments, along with CE 399 ( including the two fragments found in the limo), when weighed and added together, would end up with a weight far greater than one bullet.
Why are you including fragments found in the limo? They never came from CE 399. The fragments deposited in Connally came from CE 399. The total mass of the six fragments deposited in Connally comes no where near to exceeding the mass missing from CE 399.