Rules-wise, essence lost prior to awakening doesn't effect your magic stat because there is no magic stat to drop.
Setting-fluff-wise, it's the same thing.
They would have less "magical potential" than the organic farm-raised sapient, but it wouldn't prevent them from awakening.
From a standpoint of character creation there are people who will argue that it means genetic heritage shouldn't drop starting magic, only starting essence, but that's just a slippery slope of "i got this installed before i awakened," which needs to be avoided.
I make it a GM call since it would be an unstated exception.