At the moment a member of the community is currently working on an enhancement to update an existing user in the properties files if that user already exists: -
In the meantime you would need to find all application-users.properties and application-roles.properties files under the AS installation and remove the user from them all so that the script can add them again. In your case it may be that you are using standalone mode and the one being detected by the script is under the domain configuration or that could be the other way round.
I foind it out myself too. The same properties exists in standalone and in the domain configuration. . And that was the problem. You must delete the user from both.