WooCommerce Variation Prices specifically changes the display format of the variation prices are displayed on the front end of your website. It doesn't let you update the actual price of the variations behind the scenes. Customers are still charged the same amount, regardless of how the variations are displayed.

If you need a way to update the price of several variations at once, then we recommend our other plugin - WooCommerce Bulk Variations. You can use it to select multiple variations for a certain product (e.g. all variations with the 'Small' attribute). After selecting the desired variations, you can then change their prices in a single action. It's much faster than updating variation prices individually.

WooCommerce Bulk Variations works perfectly with WooCommerce Variation Prices.