Removing certs of unused domains will be added in one of the next releases. At the moment you have to use "certbot delete" command (or delete the corresponding files in the subfolders of /etc/letsencrypt by hand. Sorry
Hi, after delete the subfolder of host cert I've lost my machine and I've to restore by backup. Apache server get error and won't start
Well, then it was obviously used ... You should only delete unused certs ... Before deleting the cert of a web, disable SSL for it (or delete the web, if no longer needed).