Is it permissible to combine the Sunnah of Fajr with the Duha prayer and the two Rak’ahs of repentance if the Sunnah of Fajr is prayed after sunrise?

It is not permissible to combine the voluntary dawn prayer (Sunnat al-Fajr), the forenoon prayer (Salat al-Duha), and the prayer of repentance (Salat al-Tawbah) into one prayer with the intention of performing all of them, because these are acts of worship intended for their own sake. Whereas acts of worship not intended for their own sake, such as greeting the mosque (Tahiyat al-Masjid) and the voluntary prayer after ablution (Sunnat al-Wudu), may be combined with another act of worship. So, if you enter the mosque at dawn while people are praying, your joining the obligatory prayer suffices for greeting the mosque.