Rules for payment are here :-
You can pay online using the Government's payment system, or you can phone the Government's Clean Air Zone team on 0300 029 8888 for assistance.
Basically, you can only pay 6 days in advance and 6 days in arrears. However, the Order is silent on what happens if moneys are paid but not used. I suspect they have just made the no refund rule up and are not in compliance with the legislation but you'll only find out if you take them to adjudication. The legislation is the Transport Act 2000 see here for the relevant section:-
An Act to make provision about transport.
and the regulations for PCN enforcement are here :-
These Regulations make provision for the civil enforcement of a penalty charge imposed in respect of a motor vehicle by a road user charging scheme made under Part 3 of the Transport Act 2000 (c.38).
I have had a quick look and there is nothing in the Act about the management of payments for road user charges. It does seem quite unfair the way they deal with payments that are not used "on the day".
As far as I can see, the email told you that your payment for road use had expired, being beyond 13 days since payment was made. It then warned you to make a payment for your car or you'd get a PCN.
