Like so many cases on here where a CC is received, but no rejection letter for previous representations, there is a well-established process to get the matter re=set to the "representations submitted" stage.
Advice first of all is - DO NOT PAY THE CHARGE CERTIFICATE !!
Once the period for payment off the CC expires, TfL can register the PCN debt at the Traffic Enforcement Centre at Northampton. They cannot begin to collect the debt until they do this. When the register the debt, they must sent the PCN recipient an Order for Recovery in the post. This adds £10 to the CC amount, being the TEC registration fee. The OfR will also include the form to submit a Statutory Declaration. (Form PE3). This allows the recipient to declare that he submitted representations, but did not receive a letter of rejection. TEC will then cancel the OfR, and the CC and the matter reverts to the "reps submitted" stage. TfL must then pass this decision to London Tribunals for a decision. Please note that the PCN is not cancelled.