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Your post is not really precise on what happened.
Just as a hint:
Windchill users (participants) are stored internally in the USERS-table, but they are also connected to a federated object. This can be an entry in AD or in a LDAP server. Once you rename the federated objects this connection gets broken and the affected users should show up as disconnected users. These users can be reconnected in the participant manager.
There are several possible answers based on what you are doing. Please help narrow the scope by providing more details about your scenario.
Is this an existing Active Directory integration, or are you migrating from WindchillDS to Active Directory?
What details about the users are changing?
How are you determining the details aren't updating, through the Windchill UI, DB queries, other?