Will the father be held accountable for the corruption of his children who live in the custody of their mother, who apostatized from Islam after the divorce, even though the father sees his children two days a week?

If the mother is a disbeliever or an apostate, she has no right to custody of the children. The father must demand the right to custody to free the children from her, and he will be held accountable for any negligence in this regard. If he is unable to do so due to the country's laws, he must strive to reform them as much as possible and pray for their guidance and righteousness, until they reach the age where the mother's right to custody is lifted, at which point he can take them and rectify what is possible.