I have product with variations based on two attributes, size and color. I need to remove x-large black and large black. I uncheck "Enabled" for both variations. X-large removed from select list, large still there but can't add to cart.
Front-end display - http://screencast.com/t/gfhcioyLd
Variation settings - http://screencast.com/t/Mkr8sNkWa