Yes. The Macbook APP will also cover the 13" MBP. You will need some flavour of documentation showing SN B has replaced SN A that you're able to fax/email to Apple. You may also need the original proof of purchase for the original Mac/APP

Once you have this, call Apple in whichever country you are in and go through to tech support or warranties and say you want to transfer your APP. They should create a case, give you the number and details for you to email/fax your required documentation though