The stock item CSV feature you’re referring to is an importer, not an updater, I’m afraid. We don’t currently have a bulk updater for stock items/suppliers. The importer will try to import the stock items in the CSV as new, which is why you get an error stating that the stock item already exists.
You can’t currently delete a stock item, only obsolete one. Nevertheless, a stock item that’s been used would never be able to be fully deleted, as then you’ll have broken references for things like ingredient recall and historic batches.
I’m afraid the only option for existing stock items is to update them individually in the ‘Suppliers’ tab on the stock item’s page. You could post a feature request for a stock item/supplier bulk updater if this is something you’d like to see in Breww.