If we buy a 15day/2 month eurorail pass and have to take the Thello train from Milan to Paris overnight. They offer a 25percent discount for pass holders. Would that count as a day of travel for using the discount?
I will let someone else respond to your rail pass question. I just have a couple of related comments.
Be very careful if you're planning to use a rail pass in France. They severely limit the number of seats available to pass holders. Consequently, there may be lots of seats available on the train, but none available to rail pass holders. That happened to me when I tried to reserve a seat a few days ahead, and the only options were to travel on a different day, or buy a full fare ticket and leave a segment of the pass go unused. It was an expensive lesson. If you use a pass in France, reserve your seats as early as possible.
I've flown from various locations in France to Milan on the discount airlines, and it was far cheaper than going by train. You can check skyscanner.com to see what's available.
Like discounts in general, the Thello discount does not require using a counted travel day on the flexipass, though travel must be within the 2-month validated window of the pass. You do need to book French TGV reservations well in advance, preferably several weeks ahead.
Before you buy any railpass, read this, from The Man In Seat 61. Then read it again: http://tinyurl.com/bkw4u6c
We took the TGV from Turin to Paris last March. We took a high-speed train from Rome through Milan to Turin, and stayed at a wonderful hotel right across the street from the Porto Susa station. The next morning we ate at the hotel buffet, crossed the street, and boarded the 7:40 TGV. Convenient, and a beautiful train ride.
The reviews of the Thello overnight train were not encouraging (including the Seat61 info). This plan worked well for us.