Auto-renewing doesn't help in this case. The
certbot renew command only checks the validity date of the certificate, not if it will be revoked soon. According to Let's Encrypt's instructions, you have to manually update the certificates with the
--force-renewal option.
They also created a file with all the affected certificate serial numbers on
their incident page [letsencrypt.org].
The text file is a whopping 1.2 Gigabytes and contains 3 million serial numbers. That is a little bit less than 3% of the total active Let's Encrypt certificate in the field. Many certificates list multiple domain names, so the number of affected domains is even higher than 3 million. That is a significant portion of the web.
The file contains all the domain names of affected sites. I am not sure if this was the wisest move of an organization which was started to increase privacy on the web. They now--without consent of the site owners--expose deliberately at least 3 million websites with a broken security certificate. And they do this after they sent a 24-hour notice of certificate take-down for a bug which has been in the source code of their system since July 25th, 2019. Yes, that is more than half a year ago. With an average renewal cycle of 2 months, more than three generations of certificates have passed since the bug was introduced. If they just had fixed the bug silently and waited another two months, all bogus certificates would have been replaced anyway without the larger community ever knowing. Because the primary reason for the fast recycle time of Let's Encrypt certificates was just that: to have a mechanism to remove wrong certificates in an expedited way.
Besides their small engineering team of just a dozen people, they need someone with experience in public relations and crisis management for this type of disasters IMHO.