Hi, I was wondering if there is any proper process of handling a stop payment on a cheque.

Reverse the check that payment is being stopped on. This will re-open the invoice/bill.
Be sure to date the reversing transaction as the same date that the reversal is dated.

You say reverse. Exactly how does one reverse a cheque?

I am guessing by the non-response there is no way to reverse a cheque but only delete it?

I entered the cheque in August and replaced it in September. I do not want to delete that information. Is there another way to keep the data?

To reverse a vendor payment

If you haven’t already read the Vendor Payments Overview, see Finding, removing and reversing vendor payments for more information.

Use this procedure only if your transactions are unchangeable. See What are changeable and unchangeable transactions? for more information.

The payment you want to reverse should be displayed. If you need help doing this, see To find a vendor payment

1. Choose Reverse Payment from the Edit menu. After a few moments, a transaction with the exact opposite amount of the payment will be displayed in the Vendor Payments window.
2. If you want, you can make a few changes to the transaction (such as the date and the memo), but you can’t change the amounts that are associated with it.

If you’re reversing a payment from a previous accounting period, consider assigning a date from that period to the transaction you just created. This will allow your reports for that accounting period to reflect the proper amounts.

3. Click Record to record the reversed vendor payment.

If the vendor payment you reversed was originally used to fully pay a purchase, a message will appear if you received a discount for paying off the purchase promptly. If this message appears on your screen, continue to step 4.

If no prompt-payment discount applied to the transaction you originally applied the payment to, you’re done -- the payment is reversed.

If a prompt-payment discount applied to the transaction you originally applied the payment to, you also need to reverse the discount. To do this, follow steps 4 and 5.

4. Display the discount in the Vendor Payments window. (You can find discount transactions the same way as you find vendor payments; look for a transaction labeled “Discount” in the Inquiry Register window.)
5. Choose Reverse Payment from the Edit menu, then click the Record button to reverse the discount.