Does the death of a father after he had abandoned prayer and then returned to it, along with his fasting on the Day of 'Arafah, people's love for him, and his body being warm at the time of death, indicate a bad ending?

What you have mentioned are not signs of a bad ending (i.e., a bad death), and praise be to Allah Who accepted your father's repentance before his death and sealed his life with righteous deeds. Therefore, strive in supplicating for him and seeking forgiveness for him. As for the reason for that (his condition), we have no knowledge of it; doctors know it.