If an order is backordered could the comments listed with the order stay with the backorder items.
Could comment entered in Order Entry stay with the invoice even if the item is backorders. Make comments dependent upon the line item as opposed to the order as a whole. If a comment is posted below the line item it will stay with the line item even if backordered.
Transfer all of the information from the original order to the backorder batch. Create a column for previously shipped items, that extends to $0.00. That way when you reprint the original order it will contain the full history of the transaction.