In Clear Books, unallocated receipts can only be allocated to invoices. If a customer overpays an invoice or sends a duplicate payment this will be recorded on Clear Books as an unallocated receipt. To clear this amount the unallocated receipt would need to be allocated to an over payments invoice. This invoice would then be reversed by creating a refund transaction.
Head to Money > Bank accounts > Unallocated Cash.
Click on the Allocate link for the appropriate amount.
Click on the Create invoice link to clear off the overpayment.
Fill in all the required fields for the invoice and click on the plus icon beside the Account drop down box.
Create a new account code, I have called this over-payments.
Please note: Use a current liabilities group for the Account type for sales over-payments, and a current assets group for purchase over-payments.
Click on the Save button at the bottom once the account code is added.
Click on the Allocate payment button .
Select the payment and type in the amount to allocate in the Allocate payment box.
Hit the Allocate button to complete.
Next head to the Money > Bank accounts menu and click on the Money out link for the appropriate bank account.
Fill in the details of the money out form.
Explain the payment using the Refund tab. Fill in the required fields and use the account code over-payments. Click on the Add transaction button to complete.