A disobedient person is afflicted with a malignant disease, so is it more befitting to begin by reminding him of dhikr and night prayers to soften his heart, then urge him to repent, or to begin by directly urging him to repent from sins?

You should first invite this person to repent from sins, using encouragement and deterrence. Remind him of Allah's mercy and His punishment, and that "the one who repents from sin is like one who has no sin." Then, advise him to rectify his shortcomings with good deeds, for "indeed, good deeds do away with evil deeds."