Abrogation in the Quran
Question

Are there any verses that have been abrogated, i.e., erased from the Quran and replaced with others? Is there any book that speaks about the verses and Surahs, i.e., whether they were put in order by the Companions or by the Messenger or by Allah, and the names of the Surahs, and so on?
Praise be to Allah.What does abrogation mean in Islam?
Naskh (abrogation) in Arabic means lifting and removing. In Islamic terminology, abrogation means lifting a ruling indicated by a Shar`i text on the basis of evidence from the Quran or Sunnah.
The wisdom behind abrogation
The concept of abrogation is based on the Quran and Sunnah, and on the scholarly consensus (Ijma`) of Ahl As-Sunnah, and there is great wisdom behind it. In most cases, the abrogation was for the purpose of making things easier for the Muslims or increasing the rewards.
Allah, may He be Exalted, said (interpretation of the meaning):
{Whatever a Verse (revelation) do We abrogate or cause to be forgotten, We bring a better one or similar to it. Know you not that Allah is able to do all things?
Know you not that it is Allah to Whom belongs the dominion of the heavens and the earth? And besides Allah you have neither any Walee (protector or guardian) nor any helper.} [Al-Baqarah 2:106-107].
Shaykh `Abd Ar-Rahman As-Sa`di (may Allah have mercy on him) said:
“Naskh (abrogation) means moving; thus the meaning of abrogation is moving those who are accountable from one prescribed ruling to another, or waiving the ruling. The Jews used to condemn abrogation and claim that it was not permissible, even though it was referred to in the Torah; thus their rejection of it constituted disbelief and was based on pure whims and desires.
Allah, may He be Exalted, has told us of His wisdom in abrogation, and that whenever He abrogates any verse “or cause[s] [it] to be forgotten” i.e., causes people to forget it and removes it from their hearts, “We bring a better one” that is more beneficial for you, “or similar to it.”
This indicates that the abrogation will not be less beneficial to you than the original ruling, because Allah’s bounty always increases, especially for this ummah, for which He has made its religion very easy.
And He tells us that whoever rejects abrogation has rejected His sovereignty and might, as He says: “Know you not that Allah is able to do all things? Know you not that it is Allah to Whom belongs the dominion of the heavens and the earth?”
As He is a Sovereign over you, controlling your affairs in the manner of the Sovereign Who is Most Merciful and Most Kind in all His decrees, commands and prohibitions, then just as there are no limits to whatever Allah wants to decree with regard to His slaves, so too no one can object to Him for whatever He prescribes to His slaves of rulings. The slave of Allah is subject to the commands of his Lord, in terms of both religious commandments and the divine decree (qadar wa qada’), so what right does he have to object?
Moreover, He is the Guardian and supporter of His slaves; thus He guides them to that which will benefit them and supports them by warding off that which will harm them. Part of His guardianship of them is that He prescribes rulings for them in accordance with His wisdom and His mercy towards them.
The one who ponders the abrogation that occurred in the Quran and Sunnah will come to know thereby the wisdom of Allah and His mercy towards His slaves, and how He helps them to attain that which is in their best interests in ways that they do not realize, by His grace.” (End quote from Tafsir As-Sa`di, p. 61)
Types of abrogation in Islam
By learning about the different types of abrogation, the questioner will find the answer to his question and more. Abrogation is of different types, which are:

Abrogation of the verses and the ruling

such as the abrogation of the ten breastfeedings which used to establish the relationship of mahram between the infant and the woman who breastfed him; both the wording and the ruling were abrogated.

Abrogation of the verses but not the ruling

Such as the abrogation of the verse which speaks of the five breastfeedings by which the relationship of mahram is established between the infant and the woman who breastfeeds him, and the verse which speaks of stoning the adulterer and adulteress.

Abrogation of the ruling but not the verses

Such as the verse (interpretation of the meaning), {And as for those who can fast with difficulty, (e.g. an old man, etc.), they have (a choice either to fast or) to feed a Miskeen (poor person) (for every day)} [Al-Baqarah 2:184]; and the abrogation of the prohibition on fleeing from the battlefield if the enemy is ten times more numerous than the Muslims or more. Thus the prohibition on fleeing when the number of the enemy was double that of the Muslims was abrogated.
Ibn `Atiyyah (may Allah have mercy on him) said:
“Complete abrogation is when both the verses and the ruling are abrogated, of which there are many examples. Also, the verses may be abrogated but not the ruling, or the ruling may be abrogated but not the verses. The verses and the ruling are two different things; one of them may be abrogated but not the other.” (End quote from Al-Muharrar Al-Wajiz, 1/131)
Shaykh Muhammad ‘Abd Al-‘Adhim Az-Zarqani (may Allah have mercy on him) said:
“The abrogation that occurred in the Quran was of three different types: abrogation of both the verses and the ruling, abrogation of the ruling but not the verses, and abrogation of the verses but not the ruling.

Abrogation of both the ruling and the verses

There is consensus on this type of abrogation among those Muslims who accept the concept of abrogation. Proof that it occurred is seen in the report from `Aa’ishah (may Allah be pleased with her) who said: Among the things that were revealed of the Quran was that ten definite breastfeedings make a person a mahram, then that was abrogated and replaced with five definite breastfeedings, and the Messenger of Allah (blessings and peace of Allah be upon him) passed away when this was among the things that were still recited of the Quran. (Narrated by Muslim, 1452). Although this report is Mawquf (attributed to a Companion) and its chain of narration ends with `A’ishah, it is deemed to be Marfu` (attributed to the Prophet (blessings and peace of Allah be upon him)) because such a thing could not be said on the basis of personal opinion; rather such matters must inevitably have been learned from the Prophet (blessings and peace of Allah be upon him). It is well known that the phrase “ten definite breastfeedings make a person a Mahram” does not exist in the Mushaf and the ruling mentioned is no longer in effect. This proves that abrogation of both the verses and the ruling is something that occurred, and if it is proven that it occurred, then it is proven that this idea is sound, because proving that it occurred is the first evidence that it is possible and sound. And the view of those who deny that the idea of complete abrogation is not possible, such as Abu Muslim [Al-Isfahani, a Mu`tazili scholar of Usul] and his ilk is proven to be invalid.

Abrogation of the ruling but not the verses

This is indicated in many verses, such as the verse which speaks of giving charity before speaking to the Messenger, which is the verse in which Allah, may He be Exalted, says (interpretation of the meaning): {O you who believe! When you (want to) consult the Messenger (Muhammad (blessings and peace of Allah be upon him)) in private, spend something in charity before your private consultation} [Al-Mujadilah 58:12]. This was abrogated by the verse in which Allah, may He be Exalted, says (interpretation of the meaning): {Are you afraid of spending in charity before your private consultation (with him)? If then you do it not, and Allah has forgiven you, then (at least) perform As-Salat (Iqamat As-Salat) and give Zakat and obey Allah and His Messenger.} [Al-Mujadilah 58:13]. The ruling mentioned in the first verse is abrogated by the ruling mentioned in the second verse, although both verses remain.
Another example is the verse in which Allah, may He be Glorified, says (interpretation of the meaning): {And as for those who can fast with difficulty, (e.g. an old man, etc.), they have (a choice either to fast or) to feed a needy person (for every day)} [Al-Baqarah 2:184]. This was abrogated by the verse in which Allah, may He be Exalted, says (interpretation of the meaning): {So whoever of you sights (the crescent on the first night of) the month (of Ramadan i.e. is present at his home), he must observe fast that month} [Al-Baqarah 2:185]. The earlier ruling was abrogated by this later ruling, although both verses remain, as you can see.

Abrogation of the verses but not the ruling

This is indicated in the authentic report from `Umar ibn Al-Khattab and Ubayy ibn Ka`b (may Allah be pleased with them), according to which they said: Among the words that were revealed of the Quran were the words, “If an old man and an old woman commit Zina, stone them both.” But we know that this verse no longer exists on the pages of the Mus-haf or of the lips of those who recite the Quran, even though the ruling remains in effect and has not been abrogated.
It is also indicated in the sahih report from Ubayy ibn Ka‘b, according to which he said: Surat Al-Ahzab was similar in length to Surat Al-Baqarah or more. [Narrated by Abu Dawud At-Tayalisi in his Musnad, 540; ‘Abd Ar-Razzaq in Al-Musannaf, 5990 and An-Nasa’i in As-Sunan Al-Kubra, 7150; Its chain of narration is authentic). Although this large amount of verses that was abrogated could not have been devoid of rulings concerning `Aqidah (beliefs) that could not be abrogated.
It is also indicated by the abrogated verse about breastfeeding mentioned under the first heading.
It is also indicated by what was narrated in an authentic report from Abu Musa Al-Ash`ari (may Allah be pleased with him), according to which they used to recite a Surah at the time of the Messenger of Allah (blessings and peace of Allah be upon him) that was as long as Surat Bara’ah (At-Tawbah), then it was caused to be forgotten except one verse of it, which is the words: “If the son of Adam were to have two valleys full of wealth, he would wish for a third, and nothing could fill the mouth of the son of Adam but dust, and Allah accepts the repentance of those who repent.” (Narrated by Ahmad, 19280; its chain of narration is authentic and was classed as such by the editors of Al-Musnad.)” (End quote from Manahil Al-‘Irfan, 1/154, 155)
Order of verses in the Quran
With regard to the order in which verses appear, the scholars unanimously agreed that the order in which they appear in a single Surah is a Tawqifi matter (divinely ordained, bound by a religious text and not subject to personal opinion), and the matter was not subject to the Ijtihad (the exertion of a jurist’s best intellectual effort to derive verdicts from Islamic sources when clearcut texts are not available) of the Companions.
Order of Surahs in the Quran
With regard to the order in which the ٍurahs appear, there is a difference of scholarly opinion concerning this matter. The majority are of the view that it resulted from the Ijtihad of the Companions (may Allah be pleased with them), although that the order of some of those Surahs was determined at the time of the Prophet (blessings and peace of Allah be upon him).
Who named the Surahs of the Quran?
With regard to the naming of the Surahs, some of them were named by the Prophet (blessings and peace of Allah be upon him), and some were named by the Ijtihad of the Companions (may Allah be pleased with them).
The scholars of the Standing Committee were asked:
Is the one who named the Surahs of the Holy Quran the Messenger (blessings and peace of Allah be upon him), or what?
They replied:
“We do not know of any text from the Messenger of Allah (blessings and peace of Allah be upon him) that indicates that he named all of the Surahs; rather in some authentic Hadiths it says that the names of some of them came from the Prophet (blessings and peace of Allah be upon him), such as Al-Baqarah and Al `Imran. With regard to the other Surahs, it appears that they were named by the Companions (may Allah be pleased with them).
Shaykh ‘Abd Al-‘Aziz ibn Baz, Shaykh ‘Abd Ar-Razzaq `Afifi, Shaykh `Abdullah ibn Ghadyan, Shaykh `Abdullah ibn Qa`ud” (End quote from Fataawa Al-Lajnah Ad-Da’imah, 4/16)
All of the above are matters that you will find in books that deal with `Ulum Al-Quran (the science of the Quran), such as Al-Itqan by As-Suyuti, Al-Burhan by Az-Zarkashi and Manahil Al-`Irfan by Az-Zarqani
And Allah knows best.