Will the father be held accountable for not dividing the endowment money, and will giving the heirs their share now clear his conscience?

The father's responsibility is not absolved by relying on a void fatwa, because the ruling of a judge or a mufti does not make lawful what is unlawful. What was taken unjustly remains a debt that must be returned to its rightful owners. If the children return the right on behalf of the father, his responsibility is absolved.