I would write to the company to inform them that only one box of chocolates has arrived, and that I am still missing the other two. I would ask them to investigate the issue and arrange for the missing items to be sent as soon as possible.
I would reply to the email and state that I was initially informed that the price was much cheaper and that there was free delivery. I would also mention that I paid by credit card based on that information. I would question the sudden increase in price and ask for clarification or for the original price to be honored.