Shepherd's staff prevents the deletion of accounts with transaction in any fiscal year and the deletion of accounts with balances. If these balances are left over, you should try to find out why these amounts have been left over, and then, move the money appropriately.
If you are unsure what to do with these balances, then moving them to an income or expense account after you've ran your year end reports, but before you've ran the year end utility will make sure that the balance is zeroed out in those accounts at the start of your new year.
By doing so, you can then inactivate the account in question. This process will work for Asset, LIability, and dedicated accounts.