Run the data integrity check in Adagio Ledger. It will list all the departments it finds in the GL for which no department has been created in the department file. You can add these department codes manually. After you have added them, you can try deleting the ones you don't want. When you delete the department in the Edit | Departments choice, you will be given an option of deleting all the accounts associated with the department. Say "Yes" and all the accounts will be deleted (assuming they have no activity).

You don't have to wait till the new year. And importing accounts will not automatically set up the required departments.