I am getting error "CWWIM4538E Multiple principals were found" at server startup. I know the cause as the local WAS admin account has its duplicate in LDAP repository. I simply wants to remove the local WAS user gracefully offline as server won't come up. I tried playing around with changing the user id info in fileregistry.xml and corresponding change in security.xml but to no avail.
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Seems that you've added LDAP into "federated repositories" and forgot to remove "internalFileRepository" which contains wasadmin as well. You can do it in profiles/dmgr/config/cells/myCell/wim/config/wimconfig.xml, where you just remove it from the realm.