I manage over 20 client domains over a dozen servers. Have letsencrypt protecting them all. The only time I needed to manually intervene after the initial domain + SSL setup was to upgrade to ACME v2. Everything generally works out of the box with Letsencrypt + Certbot.
The real issue was a deprecated protocol, one that - as far as I know - could have been kept running at zero cost to LE because it already worked just fine.
The answer for me each time has been the age old turn it off and on again with redoing the install (or changing the way I utilised it in docker completely) and I have just found the whole thing more hassle than SSL certificates ever were.
The former can't imagine the latter are anywhere near competent, it could obviously never happen to them so the person experiencing the problem must somehow be at fault.
It's the message board equivalent of 'can't reproduce', closed.