If I book multiple flights as part of one Booking, will all flights participate in the MyUPGRADE program?

No, not all flights operated by Air Astana are part of the MyUPGRADE program. However, the flights chosen to participate in the program will change from time to time, depending on expected demand.  Use the promotional page on www.airastana.com to check if the flight you booked on the date you booked is participating in the program.