Are there verses that have been abrogated from the Qur’an and replaced with other verses? And is there a book that discusses the order of verses and surahs, and whether their arrangement was from the Companions, or the Messenger, or Allah, and about the names of the surahs?

Abrogation (Naskh) is the removal of the ruling of a legal text or its wording by evidence from the Qur’an or Sunnah. It is established in the Qur’an, Sunnah, and the consensus of the People of Sunnah. It has several types: abrogation of both recitation and ruling (such as "ten well-known sucklings"), abrogation of recitation but not the ruling (such as the verse of stoning for the elderly man and woman), and abrogation of the ruling but not the recitation (such as the verse of ransom for fasting).

The arrangement of verses within a single surah is tawqifi (ordained by the Prophet, peace be upon him), while the arrangement of surahs and their naming was mostly based on the ijtihad (independent reasoning) of the Companions, may Allah be pleased with them.