

Forgive my ignorance as I am very new to networking. Does it not look like it is the other way around? Your certificate manager tries to connect to Let’s Encrypt and fails? Even with DNS challenges, your certificate manager has to tell Let’s Encrypt to check your DNS records somehow.
This might not be what you are looking for but in such cases I just use GParted running on a Linux Mint bootable thumb drive.
Though I don’t know if a similarly capable CLI alternative exists for headless servers.