If the login attribute from an OTRS sync and the login attribute from LDAP are the same, the users should be merged.
e.g. in OTRS we have users with their email address (respectively their userPrincipalName) as login and we changed the order of attribute searching in ( lib/ldap/user.rb ) to return the userPrincipalName first.
For zammad and OTRS, the users come from the same directory, which is probably a very common scenario, right now it looks as if the users are both imported, but with different user ids, which messes up the user base completely.
I did not fully understand yet what happens, but a user merge would be desirable.