I have the same problem when going from a sales order to an invoice.  If we manually override a price on a sales order and turn it into an invoice, the price changes to whatever is set in the price rule.  I shouldn't have to create a separate price rule for each sales order i want to give a special price to.  the price on the invoice should be the same as what's on the sales order, whether I type it in manually or it comes from the price rule that was set up.  Quickbooks really needs to find a solution to the problem, it causes for many pricing mistakes and is very frustrating.