I am sorry, but I seem not to understand what exactly is the problem here:

The COD order payment records that you see in the admin are clearly 
indicating that it is COD with balance of 0 - meaning you haven't received 
any payment.
The generated invoices from the 'Product Orders' section have the full due 
amount calculated for the customer:

*Subtotal: £30.57*
*Shipment charge: £5.00*
*Tax: £6.11*
*Total: £41.68*
*Payments Made - £0.00*
*Balance Due £41.69*
*
*
*Payment total £41.68 due to:*
*Accounts Receivable*
*...some address*

Later on when you have received the payment you can manually change the 
amount in the corresponding 'Order Payment' record and then the generated 
invoice will be indicated as 'Paid' with 0.00 due amount:

*Subtotal: £30.57*
*Shipment charge: £5.00*
*Tax: £6.11*
*Total: £41.68*
*Payments Made - £41.69*
*Balance Due £0.00*
*This invoice has been paid in full. Thank you for your business!*

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