Creating certificates with --nginx works. Renew or certonly doesn't

We are trying to correct the problems preventing it from renewing...

If it fails now, it will fail later too.
[we will get it fixed for you]

Today, no more than staging vs production.
[all else is exactly the same - both should be forced to use HTTP-01 right now]

Yes, cleaning up the certs and unused files it a very good start.