1. In Configuration, click Business Rules
  2. Highlight Invoice.
  3. Under Duplicate invoice criteria, Add Invoice number to Field Name column
  4. Add 20 (or some other large number) to Length column. *
  5. Remove additional criteria that exists in other rows by right-clicking and selecting Delete row. *
  6. Check box for Automatically check for duplicate invoices
  7. Choose an option from the drop down box for Warn user or Do not allow duplicates

*Adding 20 to Length is telling The Financial Edge to match the Field Name up to 20 characters. If an invoice number is very long, and Length is set to a smaller number, duplicates may still occur. 
*If additional criteria rows are added, the filter becomes more narrow and duplicates may still occur