During this battle, you will have only Lyner and Aurica available in your party, so take special care. Flute is a rather fast enemy, and has access to a total of four attacks: Crescent Slash, which causes physical damage; Haze Attack, which has a high probability of dealing a critical hit; Snake Bite Needle, which causes Sleep and Poison, and finally, a Lv. 1 Stored Attack called Triple Blade Scatter, which deals large physical damage.
As noted above, you will only have a vanguard available for this battle, which can make him a dangerous opponent if he manages to poison and put Lyner to sleep with Snake Bite Needle, which will render you unable to attack and Guard Aurica if he tries to attack her. Therefore, you will have to hit as fast and hard as you can to make this battle as short as possible.