If you did not specifically purchase a park to park ticket, I doubt you would be able to use your day 3 ticket to ride the Hogwart's Express. I say this because your ticket will be scanned by the employees as you enter the train station. If you don't have a park to park ticket, they will not let you through (although, you can upgrade your ticket there).
If I were you, I would visit a guest relations or ticket sales window prior to entering the park the first time. That third day has a monetary value. They may be willing to apply the difference in cost between a 2-day ticket and a 3-day ticket as a credit to swap your ticket over to a 2-day park to park ticket. That might reduce the cost of a 2-day park to park ticket. I found the Universal employees to be very helpful when it came to sorting out the best "deal" and making sure it was applied to my purchase.
