Flagging an Employee using Script?

Here is the problem i am faced with:   on our sales order there is a custom check box on the line items that will alert our A/R person to remove that line when it becomes an invoice.  This is becuase we are a service company that leaves notes in the lines for our crews. We check this box when we want that line to be internal only.   when that sales order gets fulfilled and billed it brings over all the notes.  How could i flag or notify the A/R person that there is a line that needs to be removed?