On a website that is password protected using Apache basic authentication to auto-renew SSL we need to make the .well-known folder to be accessible without password.
Password protected Apache website:
<Directory "/var/www/html/"> AuthType Basic AuthName "Password Protected" AuthUserFile /etc/apache2/htpaswd Require valid-user </Directory>
Allow .well-known without password:
<Directory "/var/www/html/.well-known/"> Require all granted </Directory>