Was du‘aa’ al-qunoot part of the Qur’an then abrogated from the text?

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.