#.htaccess WildCard SSL
RewriteEngine On
RewriteCond %{HTTP_HOST} ^subdomain.example.com$
RewriteCond %{REQUEST_URI} !^/subfolder/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /subfolder/$1
RewriteCond %{HTTP_HOST} ^subdomain.example.com$
RewriteRule ^(/)?$ subfolder/index.php [L]

denermisiniz.

Ama mutlaka önceden yedek almayı ihmal etmeyin.