You need to fix the configuration files that Certbot broke. Upgrading to a newer version won’t automatically do that; it just won’t break them again in the future. You might as well fix them now, before you upgrade, and then you will be able to renew your certificates, without upgrading.
If you can avoid the conditions that would break them again, you don’t even need to upgrade.
If you decide to upgrade Certbot now, before a newer package becomes available in the PPA, I’d suggest using certbot-auto.
The Certbot installation from the PPA has installed a systemd timer named certbot that will automatically renew using the Certbot installation from the PPA. If you create a separate installation of Certbot, you’ll have to do something about that – uninstall the package, systemctl edit the timer to use the other installation, or deactivate the timer and set up your own timer or cron job.
Thanks for your detailed help mnordhoff. I thought it would have been easier to update the ppa. So your answer to me is just a workaround, not a solution. Nevertheless, the issue is now settled.