I have a website that requires a Let’s Encrypt certificate.
All other sites on the server work fine with LE, except this one.
It would be due to access from LE to the website, since it is locked down in .htaccess.
How can I whitelist LE using .htaccess?
You can't, because LE can be trying to access your site from anywhere. For each host for which you want a cert, for the HTTP-01 challenge, http://$HOST/.well-known/acme-challenge must be accessible to the public. If you're unable or unwilling to set up your server that way, you may want to look into using the DNS challenge instead.
Thank you for the reply.
The domain along with the others are located on a cPanel server making use of AutoSSL.
Is there a way of changing the challenge to DNS with the cPanel plugin?