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This is my recommendation for your issue. You can use Shopify Bulk Edit to edit the cost per item. Please follow these steps for editing:
For more information, please take a look at this guideline from Shopify here.
Hope my answer is helpful for you.
Have you tried AppJetty CommerceXpand?
It’s a collection of Shopify apps like Bulk Product Editor, Product Bundles, Sticky Cart, Countdown Manager, Back in Store Alerts, and more.
As per your requirement, you can bulk edit thousands of products in one go. Besides, you can streamline your entire business operation. You won’t need any additional app if you have this one.
You can learn more about it here - CommerceXpand for Shopify.