First advice is not to pay the Charge Certificate. This is sent out by their computer after the time period following their apparent email rejecting your reps was sent. However, I'm suspicious of what they say because I would have expected such an important letter, and it has to be a letter, to be sent by post.
Fortunately, there is a process which caters for things like this which are unfortunately very common nowadays. You wait for them to post you an Order for Recovery, (OfR). This raises the amount by £10 being the Traffic Enforcement Centre (TEC), registration fee for registering the PCN and debt. Until they do this they can take no action to collect the money, as it has not been authorised by a court. TEC is a form of county court, but without judges or courtrooms. BTW there is absolutely NO CHANCE of a CCJ being granted in the process.
Included with the OfR will be the form to submit a Witness Statement (Form TE9) in which you can report one of three things, one of which is that you submitted representations but did not receive a rejection notice.
It is very important that you now be proactive and check with TEC about every 10 days from the end of the payment period shown on the Charge Certificatenow on whether the PCN has been registered. Once it has, you can download the form from the TEC wewbsite. Don't be mislead about references to Dart CHarge or Mersey Gateway; your PCN is issued under the Transport Management Act 2004, which means you must submit a WItness Statement, the other London-specific Act under which other PCNs are issued demand use of a Statutory Declaration, a whole different process.
If you are able to view your PCN on the TfL website, and the current penalty, it will be showing £240, and this will become £250 when the debt is registered. You can, of course, wait for OfR in the post, but we have seen too many people not receive this and suddenly find bailiffs at their door. So best to keep checking regularly. Never rely on TfL or, indeed, London councils to do the right thing, they often don't.