Specific Autoinvoice Exception problem

 We have a Sales Order type that auto-applies a discount of 100%, resulting in order total of $0.00.  Recently a user created an order of this type and the, mistakenly, manually applied a 2nd discount. This resulted in a negative amount.  The order was processed and shipped and the error only caught when it kicked out on the Invoice Exception report.  Error = #11902 "amount cannot be negative when object type is positive". I went to that line item in the Interface Lines, changed the amount to $0, saved, re-ran autoinvoice.  Received new error #11930 amount supplied cannot be less that price x quantity.

What is best practice for resolving this?