Recently tried re-issuing one of the SSL Certificates, it returned a 404 error. Upon further inspection in server's error logs, is said:
[Fri Feb 17 13:16:06 2017] [error]: File does not exist: /home/www/website/.well-known/acme-challenge/random_big_string
After troubleshooting, the issue turned out to be a htaccess setting which disallowed accessing anything starting with a dot ( in this case .well-known )
- Check if the path exists
- Check if that path is writable by php
- Ensure that the path is accessible via Internet ( for LetsEncrypt to communicate ).
- If it still does not work, check for anything rejecting that request in logs (More often than not, it might be .htaccess rules, get it checked)