Use a needle and poke a very small hole in the center of the bubble. Use a sealing iron and iron from the edges of the bubble toward the hole, forcing the air out. Done properly, the hole will not show or barely show..

You'll need to experiment for the right temperature. Too much heat causes the adhesive on the covering to give off gas which creates bubbles. You want to find the temperature that will adhere the covering to the balsa, but not create gas bubbles.