Several days ago I witnessed strange problem when renewing LE certificate for cheng-tsui.com domain.
The certbot (Ubuntu 16.04, certbot 0.31.0-1, installed from its repository) ran (via Cron job) without apparent errors, yet certificate files remained unchanged until I manually ran the certbot in standalone mode.
I haven’t seen such a behavior earlier. The exact command used to renew certificates on that system:
certbot renew --webroot --webroot-path /var/www/letsencrypt/
(all corresponding changes have been made to Nginx configuration to allow accessing /.well-known/ based URLs; if required, I’ll post those configuration parts)
Other domains on the system were unaffected by this quirk.
All the certificates on the system were initially created using ‘–standalone’ authenticator.