We just went through a Sales Tax audit:  To ensure compliance with Sales Tax remittances in your jurisdiction, my advice is to mark down the RETAIL price directly in the invoice so that your QB software can recalculate the proper sales tax due.  Since you already remitted the higher sales tax, this adjustment will reduce your future sales tax liability and all will be well if you are ever audited.

You can always put a note inside the invoice to this effect (to preserve the history of the invoice) for future on-lookers.