There was a valid reason to falisify Amanda's death. It would stand to reason that WY might want to keep Ripley's return a secret, so that they can keep her focused on debriefing them on the Alien. Also they may want to avoid Ripley going to the media and exposing what WY did. By keeping all hope and motivation to reach out to anyone including her daughter suppressed, WY can keep a lid on things.
Who knows what WY did to Amanda? Maybe she's frozen in a capsule herself?