i have the same problem too. When i see the certs are expired i go to the letsencrypt plugin and do a renew,
but with the message "Cert not yet due for renewal".
After the command was issued, i get the notice that the configuration has changed, and i need to confirm,
like i have to do if i change any omv config. After i do that, the nginx config is reloaded with the right new cert.
Maybe there is a problem with the automatic reload after cert renewal by the cronjob