Be sure to set the server_protocol System Setting to https if you haven't already.
I have this in .htaccess. It's just below the www / non-www code and above FURL section. You might only need the first and last lines (though I don't think the others will hurt anything).
RewriteCond %{SERVER_PORT} !^443
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
RewriteCond %{REQUEST_URI} !^/\.well-known/acme-challenge/[0-9a-zA-Z_-]+$
RewriteRule (.*) https://yoursite.com/$1 [R=301,L]
