Let's Encrypt certificate not issued for main domain after it has been renamed
Let's assume we have a main domain test.example.com with a www. auto-subdomain active (so we have an alias for www.test.domain.com) for a web site in ISPC. After testing is done, rename it to example.com (auto www. subdomain active). Now activate SSL, Let's Encrypt SSL and save the web site config. The bug: the certificate is requested and generated for www.example.com only, and not for the main domain example.com.
I quickly had to bring the site alive, so I backed it up, deleted the old site and the bogus certificate, created a new site for example.com, activated SSL and restored the backup. With the new site (no renaming involved) LE SSL generation works fine as usual, certificate is generated for example.com and www.example.com.