Hi,
HikaShop is made to handle several carts so that in the future, you could save them, restore them, delete them etc.
When you don't have a cart loaded, HikaShop tries to load your latest cart.
When you delete all the products from your current, you cart is deleted. Then, when the system tries to display the cart, it loads the latest one if possible, which means that it would reload the cart A, as you experienced.
If you don't want that to happen, you should configure the "cart retaining period" and "Frequency of the check for the carts" options of your configuration to a really small number so that the carts are removed rapidly.