If you have a .htaccess in the root of your application, that adds a htpasswd based auth password for the entire site, the Let's Encrypt autorenewal process fails. The process create a subdirectory, .well-known/ and uses it for the renewal process, deleting it at the end of the process.

There are two easy ways to get around this that I can think of:

1. do not delete the .well-known directory at the end of the process. so that us customers can add in the .htaccess file in there if we want to, to leave it readable



2. 
   

   as a part of the process of creating the short-lived .well-known directory, add a .htaccess file in that folder with the content:

   Satisfy Any
   Order Allow,Deny
   Allow from all

   
   

And delete it all at the end of the process, as it does now. This will unlock that directory during the process automatically