What is the validity of the disbelievers' claim that the Qur’an has been distorted, citing the verse of stoning (rajm) which was not written down, and the absence of al-Mu’awwidhatayn in the Mushaf of Ibn Mas’ud, and are there any manuscripts of the Qur’an written by Uthman to this day?

Islamic legislation has undergone several stages of abrogation (Naskh), which is the lifting of a prior legal ruling by a later one. The Jews denied abrogation, claiming that it indicates the emergence of an opinion after it had not existed. However, the Quran refuted them in His (Allah’s) saying: [Whatever verse We abrogate or cause to be forgotten, We bring forth [one] better than it or similar to it. Do you not know that Allah is over all things competent?]

Abrogation is divided into three types: 1. Abrogation of recitation while the ruling remains: like the verse of stoning. 2. Abrogation of both the ruling and the recitation: like the phrase "ten known sucklings make unlawful" from the hadith of Aisha. 3. Abrogation of the ruling while the recitation remains: like the abrogation of the ruling of the verse [And those who are taken in death among you and leave wives – for their wives is a bequest: maintenance for one year without turning them out] by the verse [And those who are taken in death among you and leave wives, they should wait concerning themselves for four months and ten days].

As for the absence of Al-Mu'awwidhatayn (the two surahs of refuge, Al-Falaq and An-Nas) in the Mushaf of Abdullah ibn Mas'ud, this does not indicate distortion of the Quran. The transmitted (mutawatir) Mushaf is the Mushaf of Uthman, and Uthman ordered the burning of other Mushafs, and the Companions agreed upon it. Copies of Uthman's Mushaf exist to this day at the Maqam of Hussein in Egypt, and there is a Samarkand copy, and a Topkapi copy in Istanbul. The Quran was preserved in memory, and the Berlin Institute, after studying forty thousand copies of the Mushafs, proved that there is no distortion in it, verifying His (Allah's) saying: [Indeed, it is We who sent down the message, and indeed, We will be its guardian.]