Firstly: 

In the answer to question no. 176972 we stated that abrogation in the Qur’an is of three types: 

1.Abrogation of the text and the ruling, such as abrogation of the ten breastfeedings that make the infant a mahram to the woman who breastfeeds him. Both the wording and the ruling were abrogated.

2.Abrogation of the text but not the ruling, such as the abrogation of the verse on stoning the adulterer and adulteress.

3.Abrogation of the ruling but not the text, such as the abrogation of the verse (interpretation of the meaning): “And those of you who die and leave behind wives should bequeath for their wives a year’s maintenance and residence without turning them out, but if they (wives) leave, there is no sin on you for that which they do of themselves, provided it is honourable (e.g. lawful marriage). And Allah is All-Mighty, All-Wise” [al-Baqarah 2:240].

Secondly: 

There is a saheeh report from Ameer al-Mu’mineen ‘Umar ibn al-Khattaab (may Allah be pleased with him) that he used to recite in his qunoot soorat al-khal‘ and soorat al-hafd in Fajr prayer, and that this qunoot may be called as-sooratayn. 

“Soorat al-Khal‘” is “Allaahumma inna nasta’eenuka wa nastaghfiruka wa nuthni ‘alayka al-khayra kullahu wa nashkuruka wa laa nakfuruka wa nakhla‘u wa natruku man yafjuruka (O Allah, verily we seek Your help and forgiveness, we praise You greatly, we give thanks to You and we do not disbelieve in You and we forsake and shun those who disbelieve in You. 

Soorat al-Hafd is: “Allaahumma iyyaaka na’budu wa laka nusalli wa nasjudu, wa ilayka nas’aa wa nahfud. Narju rahmataka wa nukhaafu ‘adhaabaka, inna ‘adhaabaka al-jadd bil kuffaari mulhaq. (O Allaah, You alone we worship and to You we pray and prostrate, for Your sake we strive. We hope for Your mercy and fear Your punishment, for Your punishment will certainly reach the disbelievers).” 

It was narrated in a saheeh report that ‘Ubayd ibn ‘Umayr said: I heard ‘Umar say qunoot in Fajr. He said: “Bismillah ir-Rahmaan ir-Raheem. Allaahumma inna nasta’eenuka wa nu’minu bika, wa natawakkalu ‘alayka wa nuthni ‘alayka al-khayr, wa laa nakfuruka (In the name of Allah, the Most Gracious, the Most Merciful. O Allaah, verily we seek Your help, we believe in You, we put our trust in You and we praise You and we are not ungrateful to You)” Then he recited: “Bismillah ir-Rahmaan ir-Raheem. Allaahumma iyyaaka na’budu wa laka nusalli wa nasjudu, wa ilayka nas’aa wa nahfid. Narju rahmataka wa nakhsha ‘adhaabaka, inna ‘adhaabaka al-jadd bil kuffaari mulhaq. Allaahumma ‘adhdhib il-kafarata ahl al-kitaab alladheena yasuddoona ‘an sabeelika (In the name of Allah, the Most Gracious, the Most Merciful. O Allah, You alone we worship and to You we pray and prostrate, for Your sake we strive. We hope for Your mercy and fear Your punishment, for Your punishment will certainly reach the disbelievers.  O Allah, punish the infidels of the People of the Book who are preventing others from following Your way).” 

This was narrated by Ibn Abi Shaybah in his Musannaf (2/315) and ‘Abd ar-Razzaaq in his Musannaf (4969). 

‘Abd ar-Razzaaq added: It was narrated that ‘Ubayd ibn ‘Umayr said: Qunoot comes before the last rak‘ah of Fajr prayer, and he stated that he heardthat these were two soorahs in the Mushaf of Ibn Mas‘ood. 

See: Salaat al-Witr by al-Mirwazi (p. 105). 

It was narrated soundly from Tawoos that he heard Ibn ‘Abbaas say: ‘Umar said Qunoot, reciting these two soorahs, before the rak‘ah. 

Narrated by ‘Abd ar-Razzaaq (3/114) and at-Tabari in Tahdheeb al-Athaar – Musnad of Ibn ‘Abbaas (1/319) 

At-Tabari also narrated (1/353) with a saheeh isnaad from Ma‘bad ibn Sireen who said: I prayed Fajr behind ‘Umar ibn al-Khattaab (may Allah be pleased with him) and he said qunoot after bowing, reciting these two soorahs. 

He also narrated (1/355) with a saheeh isnaad from ‘Abd ar-Rahmaan ibn Abza, who said: I prayed with ‘Umar ibn al-Khattaab (may Allah be pleased with him) and he said qunoot, reciting the two soorahs:

“Allaahumma inna nasta’eenuka wa nastaghfiruka wa nuthni ‘alayka wa nu’minu bika wa nakhla ‘u wa natruku man yafjuruka. Allaahumma iyyaaka na’budu wa laka nusalli wa nasjudu, wa ilayka nas’aa wa nahfid. Narju rahmataka wa nakhsha ‘adhaabaka, inna ‘adhaabaka al-jadd bil kuffaari mulhaq (O Allah, verily we seek Your help and forgiveness, we praise You, we believe in You, and we nakhla’u and forsake those who disbelieve in You.O Allaah, You alone we worship and to You we pray and prostrate, for Your sake we strive. We hope for Your mercy and fear Your punishment, for Your punishment will certainly reach the disbelievers). 

Thirdly: 

In the answer to question no. 178209 we stated that this du‘aa’ may have been included in the mushafs of some of the Sahaabah (may Allah be pleased with them), but not in the sense that it is part of the Qur’an which was confirmed the last time it was reviewed with Jibreel, because the mushafs of the Sahaabah also contained commentary and fiqh, and things that had been abrogated. These two soorahs were part of the Qur’an that had been revealed then abrogated, but some of the Sahaabah continued to recite them in qunoot, because of the meanings they contained of supplication and praising Allah. 

Az-Zarkashi said in al-Burhaan (2/37): The leading hadeeth scholar Abu’l-Husayn Ahmad ibn Ja‘far al-Manaadi said in his book an-Naasikh wa’l-Mansookh, concerning that which has been abrogated from the Qur’an but was not erased from what people had learned by heart, that this included the two soorahs that are recited in Qunoot in Witr prayer. He said: There is no difference of opinion among the earlier scholars that these two soorahs were written down in the mushafs that were attributed to Ubayy ibn Ka‘b, and it was narrated from the Prophet (blessings and peace of Allah be upon him) that he recited them, and they were called the soorahs of al-Khal‘ and al-Hafd. End quote. 

See: ad-Durr al-Manthoor (8/695-698) 

The most that may be said concerning this matter is that the du‘aa’ of Qunoot was part of the Qur’an in the beginning, then it was abrogated from the Holy Qur’an, but the text remained because all of the Sahaabah were using it. 

With regard to the ugly allegations of the enemies of Allah – the missionaries, atheists and Raafidis –that this is regarded as casting aspersions on the Qur’an, and that the Ahl as-Sunnah differ concerning it, and you will see some of them adding to this argument, this is pure fabrication, because affirmation of abrogation in the Qur’an is something well-known and well-established in Islam. No one denies it except one who is ignorant or arrogant. Once this is established, the most that can be said about this matter is what we have said above, that this was Qur’an then it was abrogated. 

For more information, please see the answer to question no. 20031 and 173268 

And Allah knows best.