Unable to get new SSL Cert for 1 subdomain site

First off, thank you for your awesome plugin! Has been a huge help to me by not having to manually deal with SSL Certificates.

I ran into a problem where I was not able to get a new SSL Cert for 1 subdomain site.
The error message was:
3rd and Final Internal Validation: Payload content (xxxxxxxxxxxxxxxx) does not match the content of https://api.ait-pro.com/.well-known/acme-challenge/xxxxxxxxxxxxxxxxxx. Either api.ait-pro.com is not pointed to this server or unavailable over HTTP due to some server-side issue. Please fix this issue and try again.

The cause of the problem was that the api subdomain has an .htaccess file in that folder and the AutoSSL plugin htaccess code was being added to that .htaccess file, which caused the AutoSSL plugin to be blocked (403 Forbidden error) from continuing to process the SSL Certificate request. .pem and .csr files were not created under my SSL Cert folder in my hosting account.

The solution was to temporarily rename the /public_html/api/.htaccess file and then request a new SSL Certificate. Everything completed normally after that. So the simple solution would be to ensure that the AutoSSL htaccess code is only added in the .well-known folder instead of any other existing .htaccess files.

Thanks again for an awesome plugin!

folder/file structure
/public_html/api
/public_html/api/.htaccess
/public_html/api/.well-known
/public_html/api/.well-known/acme-challenge