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If you don't want the selected schema to be used as the default schema for these database, you can disable this behavior in the Properties tab for the connection, in the SQL Commander category.

Configuring the Initial Values

When a new Database Connection is selected, the initial values for the Database and Schema lists are by default based on the default values for the connection. You can change this behavior in the Properties tab for the connection, in the SQL Commander category. The initial value for each list that is applicable for the database type can be set to one of The Connection Default, None or The Most Recently Used.