How does Drupal handle non Drupal sub directories?
The default .htaccess file has these lines in it:

# Pass all requests not referring directly to files in the filesystem to
# index.php. Clean URLs are handled in drupal_environment_initialize().
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^ index.php [L]


So Drupal will only attempt to take control of a path if the file or directory doesn't already exist. All requests to your flat HTML site should be served without Drupal getting involved. 

Maybe you've got some 404s in your flat HTML site? If they point to a folder underneath the web root that might explain why Drupal is getting hit.