Are you using the Correct, Cancel or Create Corrective Credit Memo function? Because even if you have changed your posting groups etc. on the customer, this will copy that issued invoives setup. In this case, you would have to Using the Create Corrective function will allow you to change it before posting, where you will need to select your new setup for the open Credit Memo.
I am curious though - it sounds weird, and I am not sure I have understood the question completely. And if I have, I find it strange. What happens when your client "cancels" a sale?
I will for this example assume your client has 25% VAT, since it's the standard of my country.
1. We have a sale for 100 revenue + 25 VAT = 125 in total
2. Credit the initial invoice, but from what you say, this will just be 125 cost, since credit should be without VAT?
This would mean we have 100 + 25 VAT in sales. Minus 125 for the credit memo, resulting in a net loss of 25 for your client, because he has to reconcile the 25 VAT on the sale.
Can this really be so?