My 3month old baby is on soy base formula now, will it effect her when she gets older and have to drink regular milk? will she have problems digisting

Usually not: It is very common for an infant to be sensitive to lactose or milk protein in infancy. Very, very few, however, continue to have this problem past 6 months. As their digestive system matures, the vast majority of infants who were sensitive as newborns and young infants tolerate dairy products and do just fine with regular milk by their first birthday.