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So in Sahih al Bukhari 6829, we get to know that the verse of stoning was not there in the Quran. Doesn’t that mean that the Quran is not preserved? Or is it that the verse was not meant to be in the Quran at the first place but the ruling was supposed to be there?

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  • The preservation of the qur'an is based on the last presented and memorized version not on former ones. This verse might no more be mentioned in the qur'an, but its practice is still confirmed by the majority of Muslims. In fact after 12 centuries none among ahl-Sunnah even doubted it until a few temporary scholars revived the discussion of sects that don't exist any more like the Khwarij and Mo'atzilites.
    – Medi1Saif
    Sep 11, 2021 at 9:19

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Asalaam alaikum

As muslims we believe without any doubt in articles of faith and to believe in the revealed books are one of them. thus there should not be any question regarding the authenticity or the preservation of quran. i will try to clarify, insha Allah.

Allah the exalted and glorified says in the quran,

Indeed, it is We who sent down the Qur'an and indeed, We will be its guardian. [15:9]

after this verse, there should not be any doubt the preservation of the quran. the only one who can protect is confirming that He will be it's guardian. one of the foremost ways of how the quran is preserved is through the sunnah of our beloved messenger Muhammad (P.B.U.H). the sunnah and quran are indivisible, sunnah is the living interpretation of the quran.

in the quran it is mentioned in more than 10 places to obey the messenger with obedience to Allah the supreme. (3:32) (3:132) (4:59) (5:92) (8:1) (8:20) (8:46) (24:54) (47:33) (58:13)

this furthure strenghtens the fact that quran is preserved very well as we believe that authentic sunnah has reached us. (obviously without authentic sunnah we wouldnt know how to pray, make hajj and perform other acts of worship and good deeds)

regarding the second part of your question, it is just as you have mentioned. Allah the most wise for reasons only known to Him has made it happen that way. i will mention a few narrations regarding this just to have more clarity, insha Allah.

Umar said : Were it not that some would say Umar has added to the book of Allah what does not belong in it, I would have written it in the margins of the Quran. [Musnad Ahmad 157]

from this narration from umar (R.A) we can know that, the verse(s) was not meant to be in the quran but the ruling in our shari'a. let's look at another narration,

Zaid ibn Thabit reported: The Messenger of Allah, peace and blessings be upon him, said : The married old man and old woman, if they commit adultery, then stone them irrevocably. Umar said, “When this was revealed, I went to the Prophet and I said: Let me write it.” Shu’bah said: It was as if the Prophet disliked that. [Musnad Ahmad 21086]

  • Al-Bayhaqi comments on this statement, saying:

In this, and what came before it, are evidence that the ruling of the verse of stoning is affirmed and its recitation is abrogated. This among matters of which I do not know of any disagreement. [ reference : al-Sunan al-Kubrá 15553 ]

i believe its worthy to mention one more quote,

  • Abu Muhammad said:

When the verse of stoning was revealed, it was memorized, acknowledged, and it was acted upon by the Messenger of Allah, peace and blessings be upon him, except that he did not have it written in the copies of the Quran, nor did he affirm its wording in the Quran. Umar ibn Al-Khattab asked about that, as we have related, and the Prophet did not obligate him to do it. [ reference : al-Muhalla 12/177 ]

from this we can understand that the verse(s) of stoning was abrogated in recitation but not in ruling. we can only speculate regarding such abrogation, only Allah the all wise and all knowing truly knows the reason(s).

may Allah the mighty and sublime grant us mercy and guide us to the straight path.

Allah knows best

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