You will need to do a general journal entry to reverse the transaction as of a current date.
More than likely there will be GST (???) on the transaction which needs to be reversed.
If you void or delete it will affect previous years and have no affect on this year.
The best way to do this is to receive the payment as per usual > then write a cheque and allocate the account to your Accounts Receivable account at the bottom split then allocate that customer to that line > this will then put the balance owing back to their account.
Feel free to contact me at firstname.lastname@example.org if you need.