I have a file for all my hosts /etc/apache2/conf.d/core2-jxn-certs.conf which is suddenly getting nightly modifications, adding a SSLCertificateChainFile line which is causing apache to not work.
A Certbot renew command does not modify the Apache config. Well, it is not designed to at least.
And, your connectware.olebrook.com cert is not yet due for renewal so I'm not sure why that should do anything. It still has 48 days remaining before expiry.
Can you upload the /var/log/letsencrypt/letsencrypt.log file? You will need to copy it to a .txt file to use the upload button on this forum post menu.
Last, what do you mean by Apache "not working". It is responding to requests to that domain for me.
Sorry I think a correction it was connectware.inn-cloud.net that renewed two nights ago, but it was the connectware.olebrook.com block that was modified with the SSLCertificateChainFile. It happened last night without a renewal, so maybe renewal isn't the trigger.
So if certbot isn't modifying that file what else would?
I am seeing a normal cert chain for our inn-cloud domain. (SSL Checker link)
That SSLCertificateChainFile is deprecated in your Apache version but Apache would not "break". It would just send more cert intermediates than needed and perhaps this would confuse certain browsers. Since the above SSL Checker sees the correct chain I don't understand what you mean by Apache "not working"