I sent exactly as advised in this thread by email and received a receipt.
Cant see where you can reply to this letter ... ?
You don't need to reply, you need to call London Tribunals on 020 7520 7200 and ask if your appeal has been registered yet. If they confirm that it has been, you can simply ignore the charge certificate.
I do know London Tribunals have had a bit of a backlog lately registering appeals, so it might be that if it's still in the queue to be processed, TFL have not been notified yet (hence the charge certificate).
The important thing is that as long as you emailed the form to the tribunal within the 28 day period, it doesn't matter how long the tribunal back office staff take to process it, the appeal was in-time and that's the end of that.
Indeed at least having emailed it you know they've received it, if you'd sent it in the post we'd have no idea if it was simply lost in the post.