There are all kinds of scenarios (e.g. fraud) where a CC refund is warranted even if you shipped the product, so without further details it's quite plausible th

There are all kinds of scenarios (e.g. fraud) where a CC refund is warranted even if you shipped the product, so without further details it's quite plausible that Stripe should have forcefully refunded the payment even taking your proof of shipment into account. Credit cards ensure that customers get all kinds of protections and in many (hopefully rare, but it depends on the industry) cases the risk falls on the merchant, that you might not eventually receive the money.