Hi Hjalte,
You can try both: https://apps.shopify.com/metafields-editor (free) and https://apps.shopify.com/metafields2 (7$/month, but has metafileds import/export feature you need).
Also I'd recommend to use some accounting system that can integrate with your Shopify store. For example, Brightpearl saves us a ton of time. It does the job of calculating all product costs for you.
