Let's Encrypt Auto-renew not working because of rewrite rule in .htaccess

My Let’s Encrypt auto-renew actions stopped working recently, and I’ve narrowed it down to this line in the .htaccess file in the root level of each domain:

# security rules: # - deny access to files not containing a dot or starting with a dot # in all locations except installer directory RewriteRule ^(?!installer)(\.?[^\.]+)$ - [F]

I’m not enough of an Apache guru to figure out how to change this rule to allow access to files in the .well-known directory as well as the installer directory.

I’m running Webmin 1.870 and Virtualmin 6.02 on CentOS 7.1