Get out of Stripe as fast as you can. I left Shopify completely to avoid Stripe. I do not trust them at all. We are losing charge backs they let through and never flagged. They do not protect their merchants at all. If you are already with Stripe and have lost charge backs I suggest you do as I just did and request Stripe provide you with proper documentation (from Visa/MC/AMEX) that you actually lost these charge backs.
I am strongly considering filing a small claims case against them or contacting a lawyer to see what I can do. So I lose the chargeback and products.
I am furious. I have since switched to Big Commerce and use Authorize.net. I use Flagship Merchant Processing and pay 1.9% on credit cards and I think .5% on debit cards. If you do not use Stripe as your processor within Shopify they take 1% of your transactions anyways.