A few years ago we did a mass update of the usernames in Windchill due to a takeover. The way we did that was to create a loader file (how to create and use them is very well described in the "Windchill Data Loading Reference and Best Practices Guide". Because of legacy, it was not possible to just change the username. Our solution was to add an alternate username. It is possible to provide a user in WindchillDS up to 4 alternate usernames.
Authentication is done at our company to Active Directory where the "new" usernames where used. After this action, user where able to log on using their "new" username.
I hope this answers your question a bit. Or steer you in the right direction.
We are looking into alternate names, however, we are using Active Directory and it does not have the concept of alternate user name, at least it isn't implemented here. I think if I can map the alternate user name to an AD user attribute, then this will work.