Doctor scared my daughter about having congenital hypothyroidism. What would you say?

Life long treatment. Approximately, 1 in 3000 newborn babies is found to have a very low level of thyroid hormone. This is generally due to either complete absence or poor development of thyroid gland. Once diagnosed and treatment (hormone replacement) started early in newborn period, normal life is expected in most of the affected individuals.
Low thyroid function. 'congenital' means it's present at birth, and hypothyroidism is when the thyroid gland (which is at the front base of the neck) isn't producing enough of the chemicals it should. This condition requires treatment with thyroid hormone to replace what the thyroid isn't making.