Note this is not an error but a warning.
It could mean that the same user exists as part of multiple ldap configs.
If a single ldap config, you command should have corrected the warning.
However, please keep in mind that for clearing the user_login_domain and user_global_unique_id, the user_name must match what is in Documentum.
If not a match, this will not work.
You would then need to update the user_global_unique_id with the exact value that you see in the report (with trace level 10)
Hope that helps
Important note: you should not rename users directly but instead use the job dm_UserRename. This job will take care of renaming various references to the user such as group and ACL entries, owner_name information on dm_sysobjects, etc.
If it's a new user who never did anything in the repository, I guess you can do it via DQL but it's cleaner via the job.