It's your fault for leaving those boots in the cart. Accept the L, return the boots, and learn your lesson. Some boutiques have a no return policy, so just be happy you can get some sort of refund for your mistake even if it is store credit. If you were going for the GLV's, you'll more than likely go for something else later on. I guess you can reject the package, but you'll probably be charged a restock fee on everything. If you really hate them now, then just return the boots and sell your coves, you'll get almost all your money back AND store credit in which you can buy a gift card for someone or something. You have all these options besides a chargeback that should NOT go in your favor.
As far as them being able to alter orders of multiple shoes, this is just speculation by me but I'm thinking it's probably because some of it may have been their fault. Reading about most multiples, it sounds like if you pressed add to cart more than once it added to cart however many times you pressed it. Most people click once and let it load, but some people probably clicked repeatedly because it was loading slow or something. Since it may have been partly their fault, they adjusted orders instead of straight canceling. Again, it's just speculation but it's the only reason I can think of why they'd adjust vs cancel orders.