I have this rule in an .htaccess file located in a directory named clips/
:
RewriteRule ^mlk/?$ segment/index.php?clip=1 [R=301,QSA,L]
Try adding a RewriteBase directive as below
RewriteEngine On
RewriteBase /clips/
RewriteRule ^mlk/?$ segment/index.php?clip=1 [R=301,QSA,L]
EDIT
but is there any way to get this to work without using a RewriteBase directive
You could also try
RewriteEngine On
RewriteCond %{REQUEST_URI} ^(/[^/]+/) [NC]
RewriteRule ^mlk/?$ http://%{HTTP_HOST}%1segment/index.php?clip=1 [R=301,QSA,L]