Also, perhaps take a quick look here:
http://doc.otrs.org/3.1/en/html/config.html#Framework:Frontend::Customer::Auth
Search for “suffix”.
With “Customer::AuthModule::LDAP::UserSuffix” you can append the UPN part to the username, and have them login with just that.
That does not solve the duplicate usernames though, I’m not sure how it will handle that, but it may be worth a shot.
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/Sune T.