Because God is outside of time, He is able to take the prayers of His faithful and apply them retroactively.
If I were you, I would begin praying daily with great fervor that your father experienced sorrow and contrition before dying. I would pray especially for the hour of his death and ask Our Lady to have held him close to her maternal heart and helped inspire him to repentance. I would ask God to give your father the gift of faith and desire for salvation during the hour of his death. I would ask God to show mercy upon the soul of your father and beg Him to allow your father salvation.
Because God has known for all of eternity that your father would leave the Church but have a faithful Catholic daughter capable of praying for him and his soul, God is perfectly willing and able to apply any prayers you have for your father to the moment in which you want them applied. I hope this is making sense. At the moment of your dad’s death, He knew that you would be troubled by this days or weeks or months later, and knew that you would pray fervently for your father’s salvation. He can then apply the prayers of you, a righteous woman, for your father’s soul at the moment when your father needed it most.
Padre Pio once heard the confession of a woman who was absolutely tormented with worry that her husband, who had committed suicide, was in hell. She asked him if he could provide her any insight into where her husband was and if he was truly in hell. Padre Pio told her that no, her husband was not in hell, because of his wife’s prayers. During the split moment between jumping from the bridge and hitting the water, the woman’s husband had asked God for forgiveness. This act of his was inspired by his wife’s prayers, though he did not understand nor realize it. He was simply in purgatory.
You have the rest of your life to allocate prayers to the hour of your father’s death. You have the rest of your life to offer prayers, masses, rosaries and redemptive sacrifices to enable him to get out of purgatory. Perhaps he will be released by the time of YOUR death, and then be a saint in heaven praying for YOUR release from purgatory someday.
Trust in God’s mercy and be grateful for the power of prayer. Your faith is still a gift to your earthly father. Use it!