Whilst they won't accept an appeal now, the usual wording recommended would be something along the lines of the below:
Dear Sirs,
I have received your Parking Charge Notice (Ref: ________) for vehicle registration mark ____ ___, in which you allege that the driver has incurred a parking charge. I note from your correspondence that you are not seeking to hold me liable as the registered keeper, under Schedule 4 of the Protection of Freedoms Act 2012 ("The Act"). You have chosen not to issue a Notice to Keeper in accordance with The Act, and it is now too late for you to do so.
There is no obligation for me to name the driver and I will not be doing so. I am therefore unable to help you further with this matter, and look forward to your confirmation that the charge has been cancelled.
Yours,
They will probably reply stating you're too late to appeal. At some point after that you'll probably start getting letters from debt collectors - these debt collectors are powerless and you should ignore them. If you receive a Letter of Claim from a law firm representing Universal, come back here for advice.