According to the last movie, RE: The Final Chapter, Alice was a clone all the way along, starting with the original 2002 film. She was cloned after Alicia Marcus to serve as a secret operative / head of security for Umbrella, at a time when the Corp. already had succeeded with cloning technologies. This is also the reason why Alice does not have any memories of her childhood or parents; she only remembers the few events preceding the outbreak, e.g. her arranged marriage with Spence, her secret meeting with Lisa Addison, and the night before the T-virus was stolen from the Hive. There was no "original" Alice to begin with, as other answers suggest.