Hi Anikesh,
Thank you for your message.
There is no such feature in the Kentico E-Commerce module, so the only solution is to ensure this with custom logic. The best place for this is probably in the ShoppingCartItemSelector control, located here:
\CMS\CMSModules\Ecommerce\Controls\ProductOptions\ShoppingCartItemSelector.ascx
In the code of this control you will need to extend the method AddProductToShoppingCart, and add a custom logic that removes all instances of the product from ShoppingCart.CartItems based on the SKUID property.