Their service of a Charge Certificate means they would appear to have ignored your late reps. Whilst it would be polite of them to tell you that you are too late, they don't legally have to do this.
It is always best in circumstances like yours to follow the legal process. However, if by some chance of fortune they accept your later reps then the PCN will be cancelled, but I doubt this will happen. The facility to submit a Witness Statement is a back-stop, for when the process has gone astray, which clearly here it has. Therefore when the period for payment of the CC has expired, you need to be proactive in checking the status of the PCN. Our usual advice is to check with TEC about every 7-10 days whether the PCN has been registered. You can also look at the amount owing on the PCN on the TfL website, because when it goes up by £10, the PCN has been registered, because the £10 is the TEC registration fee. Once it has, then you can submit your Witness Statement. You can download the form from the TEC website, but if you receive the Order for Recovery in the post, the WS form will also be included.