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.
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.