RewriteRule ^(.*)$ index.php [L]
RewriteCond %{SCRIPT_FILENAME} !-f
RewriteCond %{SCRIPT_FILENAME} !-d
RewriteRule ^(.*)$ $1.html [L]

The first rule rewrites everything to index.php. The directives that follow are effectively ignored.

However, the second rule also rewrites everything (same pattern ^(.*)$ - obvious conflict), that doesn't map to an existing file or directory to append a .html extension. This second rule is more restrictive.

It seems that what you want to do is:

1. Append the .html extension to URLs that would map to .html files.
2. Rewrite all other requests that (I assume) do not map to physical files and directories to index.php.

Additional assumptions

• The .htaccess file is located in the document root.
• Requested URLs that should map to .html files do not contain dots in the URL-path. Therefore, dots in the URL-path indicate file extensions only.
• If you literally rewrite everything else to index.php (as you were doing) then it will also rewrite all your static resources (CSS, JS, images, etc.), so I assume you want to make exceptions for static resources and anything that would otherwise map to a file or directory.

Try the following instead:

RewriteEngine On

# Append the ".html" extension if the target file exists
RewriteCond %{DOCUMENT_ROOT}/$1.html -f
RewriteRule ^([^.])$ $1.html [L]

# Rewrite other requests that don't map to files/directories to index.php
RewriteCond %{SCRIPT_FILENAME} !-f
RewriteCond %{SCRIPT_FILENAME} !-d
RewriteRule !\.(?:css|js|jpg|png|gif)$ index.php [L]