Well, you can't really
practice the flute, but I guess you could practice technique. I guess this only (or probably only) applies to more experienced players...but you could work on double tounging, tuning exercises (singing helps) or breathing exercises, or flutter tounging. If you really wanted to be creative, you could just get a pencil or something and practice fingerings if you need to work on a run or something. Other than that, technique is really the only other thing you could practice.
you could also practice reading the music and learning different fingerings or blowing on a bottle to practice how to blow in a flute