I renamed four existing Ploi sites and reissued their SSL certificates. Immediately afterward, /etc/letsencrypt/live and /etc/letsencrypt/archive contained only those four newly issued certificate lineages.

Approximately 45 unrelated enabled sites still have renewal configuration files and Nginx SSL references, but their corresponding live and archive directories are missing.

Examples:

• /etc/letsencrypt/renewal/admin.oneapp.sa.conf exists.
• It references /etc/letsencrypt/archive/admin.oneapp.sa.
• That archive directory no longer exists.
• certbot certificates reports expected /etc/letsencrypt/live/admin.oneapp.sa/cert.pem to be a symlink.
• nginx -t fails on missing certificate files.
• The currently running Nginx process still serves the sites because the old certificates appear to remain loaded in memory.

Please investigate whether the rename/reissue operation removed unrelated Certbot lineages and advise whether Ploi has a server-side backup or recovery mechanism for /etc/letsencrypt/live and /etc/letsencrypt/archive.

Please do not restart Nginx while investigating, because the current configuration cannot reload successfully.