I have, for example /var/www/sub1.site.tld/ssl, with acme (LE) certs. That ssl folder contains files: sub1.site.tld-le.crt sub1.site.tld-le.key sub2.site.tld-le.crt sub2.site.tld-le.key sub3.site.tld-le.crt sub3.site.tld-le.key Every sub.site/tld/ssl folder has all of the cert files for all of the other subdomains on that domain.tld. What's going on? This is 3.2.12 ... might an update to 3.3 help to purge those files and avoid this duplication and mis-location of files? Thanks
Default is a san certificate is created containing all domains and not separate certificates for each domain. Have you checked "Create aliasdomains as web site" under System >> Interface configuration? Default is off. It's the only posible explanation I can think of.
As mentioned in your other posts, this happened because you switched from certbot to acme.sh during migration, which is generally not supported. Use the same Let's Encrypt client on the new system when you migrate a server.