I've just gave a little more thought to your case. I don't see a way to export orders with cost prices of producs as native Shopify export doesn't allow to export metafields. How you suppose to export product cost prices in respect to orders? You'll have to maintain some other database of product costs.
As of metafileds2. Just install it, go to configure, add new field for product, go to settings (gears icon in the right top corner), export cvs sample, paste your cost prices there and import that csv back.