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I try SQL Developer 4.0 and 4.1, both old and new installation have the same list of the LDAP Server.
I have changed the ldap.ora file on ORACLE_HOME/network/admin folder from old list to new list. But the SQL Developer still use the old list.
On "New / Select Database Connection" window --> Select 'LDAP' from the "Connection Type" --> on "LDAP Server", click the arrow button, it will show the list.
My question is: Where the list items coming from?
Have you tried just searching your machine to find ALL of the locations that it MIGHT BE coming from?
Then rename those locations until Sql Dev can no longer find it and that is the source.