Hi,
You can potentially do it with the mass action system in System>Mass actions.
You can create a new one with a filter on the column product_parent_id equal to the id of the product for which you want to delete the variants, and with an action "delete the elements".
When you click on the process button, it will delete the first 500 elements (you can increase that to 2000 and it should still work in the limitation area). Repeat the process button until there are no variants left and you'll then be able to access your product and reconfigure it.
Otherwise, if you want to clear all your products in a fast way, go in your phpmyadmin and empty the tables hikashop_price, hikashop_product, hikashop_variant, hikashop_product_category, hikashop_product_related and hikashop_file.