Hello,
We have an app for you that can manage your inventory from Amazon to Shopify, and vice versa. You can list your Sopify products onto Amazon, and sync inventory quantity from your Shopify store to Amazon, and you can choose to synci inventory quantity from Amazon back to Shopify. You can choose to enable or disable that, so I believe that will resolve the issue you are having with inventory. Check out our app at http://apps.shopify.com/product-feed-manager
