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>