Any update with this issue? I am experience similar issue.
the generated .htaccess clearly shows the folder or blog that was generated by it.
Should this plugin be generated at the root level? or do you need to place each generated site login info into the .htaccess?
ex:
# HIDE-LOGIN
RewriteEngine On
RewriteBase /
RewriteRule ^foo-logout example/wp-login.php?action=logout&_wpnonce=78475b5ba8&hide_out_key=0adG0jNA [L]
RewriteRule ^foo-logout example_2/wp-login.php?action=logout&_wpnonce=78475b5ba8&hide_out_key=0adG0jNA [L]
RewriteRule ^foo-bar example/wp-login.php?hide_in_key=AJcAce0&redirect_to=https://blog.mysite.com/example/wp-admin/ [R,L]
RewriteRule ^foo-bar example_2/wp-login.php?hide_in_key=AJcAce0&redirect_to=https://blog.mysite.com/example_2/wp-admin/ [R,L]
RewriteRule ^foo-admin example/wp-admin/?hide_admin_key=LARa [R,L]
RewriteRule ^foo-admin example_2/wp-admin/?hide_admin_key=LARa [R,L]
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example/wp-admin
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example_2/wp-admin
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example/wp-login\.php
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example_2/wp-login\.php
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example/foo-bar
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example_2/foo-bar
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example/foo-admin
RewriteCond %{HTTP_REFERER} !^https://blog.mysite.com/example_2/foo-admin
RewriteCond %{QUERY_STRING} !^hide_in_key=AJcAce0
RewriteCond %{QUERY_STRING} !^hide_out_key=0adG0jNA
RewriteCond %{QUERY_STRING} !^hide_reg_key=AHyFz9nA
RewriteCond %{QUERY_STRING} !^hide_admin_key=LARa
RewriteRule ^wp-login\.php https://blog.mysite.com/example [L]
RewriteRule ^wp-login\.php https://blog.mysite.com/example_2 [L]
RewriteCond %{QUERY_STRING} ^loggedout=true
RewriteRule ^wp-login\.php https://blog.mysite.com/example [L]
RewriteRule ^wp-login\.php https://blog.mysite.com/example_2 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
# END HIDE-LOGIN