How does a Muslim reconcile the Hadith: "He is subject to Allah's will; if He wills, He will forgive him, and if He wills, He will punish him," with the acceptance of repentance and the saying that "the one who repents from sin is like one who has no sin"? And will the punishment be in the grave or in the Hereafter? And does Allah accept good deeds from a repentant sinner?

There is no contradiction between the texts that made forgiveness dependent on God's will and the texts indicating the acceptance of a repentant person's repentance. The former applies to one who meets God with a sin, whereas the sin of one who repents sincerely is forgiven by God's permission. Punishment, whether in this world, the grave, or the hereafter, is up to God, and He may forgive it. The questioner is advised to have a good opinion of God and not to despair of His mercy.