Doesn't the verse of stoning, which is alleged to have been removed, contradict God's preservation of the Qur'an?

The abrogation of the Quran does not contradict its preservation. The stoning of the married fornicator was something recited in the Quran, but Allah abrogated it as a test, and scholars have reached a consensus on it. Abrogation is a known matter in Islam, and Allah Almighty said: "Whatever a verse We abrogate or cause to be forgotten, We bring forth [one] better than it or similar to it" and "And when We substitute a verse in place of a verse." Abrogation is mentioned in the Quran and Sunnah, and one of its types is the abrogation of recitation while the ruling remains, such as the verse of stoning. This statement is not a claim of deleting a verse from the Book of Allah, but rather it is what the texts of revelation indicated and upon which the scholars have reached a consensus.