Hi Don,
Did you ever come up with a way to fix your problem? I have a similar issue. What I've done is credit the sales tax and apply the credit to the invoice. Since we have a Tax Schedule ID set up for exempt sales, I processed a zero dollar invoice and entered the correct exempt Tax Detail ID with the sales amount and the taxable sales amount. This seems to take care of the tax reports. I believe you should be able to do this with debit and credit memos, as well.
Kim