The Mus-haf (Quran) that we have today is that on which there was consensus among the Sahaabah
Question

Is it true that there are verses that were recited at the time of the Messenger of Allah (blessings and peace of Allah be upon him), then they were not included in the Mus-haf (Quran) that we have today? Is there in that an indication that the Quran that we have now is not the same Quran that existed at the time of the Messenger of Allah (blessings and peace of Allah be upon him)? Is it possible to explain about the abrogated verses that no longer exist in our Mus-haf? I have heard that there is a verse called the verse of stoning, and that it was part of the Quran, then it changed and became part of the Sunnah; its recitation was abrogated but the ruling remained. If its ruling still remains in effect, what is the wisdom behind abrogating its recitation? In other words, how could it be abrogated and no longer recited as part of the Quran, but the ruling was not abrogated? Does this mean that the Sahaabah (may Allah be pleased with them) differed concerning the Quran? Otherwise, what do we understand from the fact that each of them had a copy of the Quran that was different from what we have today?
Praise be to Allah.Firstly:
First of all, we would like to share with the questioner our experience with this type of inquiry, because we have found that those who are behind such queries are usually people who specialize in mixing issues in order to cause confusion, and try to reach a definite conclusion that the idea of the preservation of the Quran is completely incorrect and unfounded, and that no one can prove whether the Mus-hafs that we have nowadays are the word of Allah, may He be glorified, or not. This is a dangerous slippery slope.
There is one idea that could prove the point, which is that even if we assume – for the sake of argument – that some verses and soorahs that were recited at the time of the Prophet (blessings and peace of Allah be upon him) were not written in the Mus-haf, for one reason or another, that does not mean that everything that has reached us of the Quran is false and incorrect – Allah forbid.
Another idea that could prove the point is the fact that by always assuming that in any process of large-scale historical transmission – such as the transmission of the Quran, the number of verses of which are in the thousands, and these verses were also transmitted by thousands of the Sahaabah, and it was written down on thousands of slates, skins, pieces of other material and so on – it is inevitable that historical reports will tell us that there were some small errors on the part of one or some of the transmitters, or there were some debates between them, or that there were small variations between others. This is something that invariably happens, without a doubt, in the process of transmission or memorization.
As for distortion, however, that is done by people of whims and desires, who try to twist the facts and try to confuse non-specialists, so they regard such issues as evidence of the Quran “being distorted”, or that its transmission process is not credible.
They forget that the Quran was transmitted to us – in the version that we have nowadays, with the same script, shape and way of writing – through hundreds of thousands of proven, sound chains of narration that are spread throughout the Muslim world, and that the copies of the Quran that have chains of narration going all the way back to the Messenger of Allah (blessings and peace of Allah be upon him) are innumerable and are housed in libraries throughout the world. If huge academic institutions were to be established to list all these chains of transmission, Mus-hafs and books, and to collect evidence to prove that the Quran was narrated via tawaatur [i.e., it was transmitted from so many by so many that it is inconceivable that they could all have agreed upon a mistake], that would not be possible.
If we think that this will undermine the credibility of the transmission of the Quran, and that makes us think that there were additions and subtractions to it, then in that case we are rejecting all the rules and standards on how to judge a text from an academic point of view, and we are dismissing all the proven ways of sound transmission, and we are dismissing all that was transmitted of the legacy and history of nations, because of one report here or there that we did not reflect upon or understand properly, and we did not know the right way to approach it. There is no criticism that was mentioned in the context of the topic under discussion, regardless of how sound and correct it may be when subjected to examination, but it would be possible to find many more criticisms like it, whether of the same type or otherwise, to that which people transmitted of reports, knowledge, history and the ancient legacy, all of which came to us through transmission. Moreover, the transmission of the Quran – and indeed, the Sunnah too – was clearly undertaken by trustworthy narraters, and this transmission is proven to be sound, in a manner that is not applicable in the case of any other book or report.
Perhaps the questioner will agree with us, that it is very strange and amazing to find someone who believes that the Quran is the word of Allah, the Creator of all things, the controller of all things, the Creator of all the wonders of this universe, to Whom belongs the dominion of the heavens and the earth and everything in between, and He has power over all things, yet despite all that he finds it unacceptable that Allah, may He be glorified and exalted, should decree that the recitation of a few verses be abrogated, or that the rulings thereof be abrogated, or that both the recitation and ruling thereof be abrogated.
Is not Allah, may He be glorified and exalted, the one Who sent down these verses, Who spoke these words, the one Who issued the rulings mentioned? So why can he not understand and accept the idea that Allah, may He be glorified, may decree that some of these words be removed from the pages of the Mus-haf, yet remain part of His holy words, just as the Torah and Gospel are words and commands of Allah, yet despite that, the Quran abrogated both of them, yet what is remains of the Torah and Gospel that has not been distorted is still to be venerated and appreciated, on the grounds that it is the word of Allah, may He be glorified and exalted?
What harm is there in any of that?
We can see an example of this issue in this world, in anyone who writes a book or composes a speech. He may take out (or “abrogate”) something that he had mentioned in his book, or he may change the order of the ideas of what is mentioned in the book. How could anyone think that this is the right of a weak, created individual, yet some people think that it is a shortcoming in the case of the Creator, may He be glorified and exalted!
If someone were to say that abrogation means that Allah realized that there were some shortcomings and problems in what was already there, then He decided to abrogate it and present the verse or soorah in a new way, the response to that is: This is proof that this person does not understand the issue of abrogation in the first place. All that abrogation of recitation means is simply that the verse is no longer part of the Quran, and that reciting it is no longer to be regarded as an act of worship, although its ruling remains in effect, or that the verse is no longer to be regarded as part of the Quran and its ruling is to be abrogated also, although it is still regarded as being the words of Allah.
It is well-known that worshipping Allah in a particular manner is a matter that is not subject to rational thinking in the first place, so how can anyone object by saying that abrogation of the recitation of the verse means that it became clear that there was some shortcoming or problem with it.
On our website, in the answer to question no. 105746 . we have given some examples of verses of which the recitation was abrogated, and we have quoted what the scholars of said about the great wisdom behind this type of abrogation.
Thirdly:
Once you understand the above, it will become clear that what the scholars of Sunnah said about the verse of stoning, the recitation of which was abrogated whilst the ruling remains in effect, comes under the heading of abrogation (naskh), which has already been discussed and guidelines concerning it have been explained above, and there is a clear reference to it in the Quran itself, in the verses in which Allah, may He be glorified and exalted, says (interpretation of the meaning):
“We do not abrogate a verse or cause it to be forgotten except that We bring forth [one] better than it or similar to it. Do you not know that Allah is over all things competent?
Do you not know that to Allah belongs the dominion of the heavens and the earth and [that] you have not besides Allah any protector or any helper?”
[al-Baqarah 2:106-107].
For more detailed information on what was narrated concerning the verse of stoning, please see the answers to questions no. 179886.
Fourthly:
Similarly, we may say that there was no difference among the Sahaabah concerning the Quran. Rather some people think that there was a dispute among them because they saw that some of the Sahaabah wrote some interpretations and explanations in their own Mus-hafs, whilst other Sahaabah were still keeping these verses of which the recitation had been abrogated. Therefore they thought – by mistake or deliberately – that this was a real difference of opinion among the Sahaabah concerning the Quran, when in fact it was not a difference of opinion at all; rather it was, as noted above, a commentary and explanation written by the Sahaabi in his own personal copy. Therefore some people distorted this fact, trying to give the impression that it was part of the Quran, or it was verses and soorahs that had been abrogated, but this Sahaabi did not erase them from his own personal copy, in order to remember them and act on the ruling, but he knew and accepted that he could not recite them as an act of worship.
For more details concerning these matters, please see questions no. 178209, 195880 and 197942.
And Allah knows best.