The purpose of this post is to show although the Quran apparently confirms substitution of some verses in place of the others, we can not find any verse that would, in fact, revoke an earlier command in Quran. In other words, even knowing that some verses has been definitely replaced, we are still unable to find any evidence, hence the Quran miraculously remains contradiction free. Therefore, we can infer that replacing some verses do not necessarily mean abrogating a previously given command.
Conversely, the skeptic would say the fact that God says he has replaced some versus and yet we can not find them is itself contradictory. The Quran's answer is stated in the verse 2:106; God may have caused it to be forgotten.
The first two verses below are considered as the proof of abrogation of some verses in Quran. The next three pairs of verses are the most famously believed cases in which the second verse is said to abrogate the first one. There are however, many other verses in Quran which are, more controversially, believed by some scholars to have been substituted by a newer one.
بِسْمِ اللَّـهِ الرَّحْمَـٰنِ الرَّحِيم
وَإِذَا بَدَّلْنَا آيَةً مَّكَانَ آيَةٍ ۙ وَاللَّهُ أَعْلَمُ بِمَا يُنَزِّلُ قَالُوا إِنَّمَا أَنتَ مُفْتَرٍ ۚ بَلْ أَكْثَرُهُمْ لَا يَعْلَمُونَ - 16:101
SAHIH INTERNATIONAL
"And when We substitute a verse in place of a verse - and Allah is most knowing of what He sends down - they say, "You, [O Muhammad], are but an inventor [of lies]." But most of them do not know."
مَا نَنسَخْ مِنْ آيَةٍ أَوْ نُنسِهَا نَأْتِ بِخَيْرٍ مِّنْهَا أَوْ مِثْلِهَا ۗ أَلَمْ تَعْلَمْ أَنَّ اللَّهَ عَلَىٰ كُلِّ شَيْءٍ قَدِيرٌ - 2:106
"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?"
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8:72 "Indeed, those who have believed and emigrated and fought with their wealth and lives in the cause of Allah and those who gave shelter and aided - they are allies of one another. But those who believed and did not emigrate - for you there is no guardianship of them until they emigrate. And if they seek help of you for the religion, then you must help, except against a people between yourselves and whom is a treaty. And Allah is Seeing of what you do".
33:6 "The Prophet is more worthy of the believers than themselves, and his wives are [in the position of] their mothers. And those of [blood] relationship are more entitled [to inheritance] in the decree of Allah than the [other] believers and the emigrants, except that you may do to your close associates a kindness [through bequest]. That was in the Book inscribed."
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2:240 "And those who are taken in death among you and leave wives behind - for their wives is a bequest: maintenance for one year without turning [them] out. But if they leave [of their own accord], then there is no blame upon you for what they do with themselves in an acceptable way. And Allah is Exalted in Might and Wise."
2:234 "And those who are taken in death among you and leave wives behind - they, [the wives, shall] wait four months and ten [days]. And when they have fulfilled their term, then there is no blame upon you for what they do with themselves in an acceptable manner. And Allah is [fully] Acquainted with what you do."
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58:12 "O you who have believed, when you [wish to] privately consult the Messenger, present before your consultation a charity. That is better for you and purer. But if you find not [the means] - then indeed, Allah is Forgiving and Merciful."
58:13"Have you feared to present before your consultation charities? Then when you do not and Allah has forgiven you, then [at least] establish prayer and give zakah and obey Allah and His Messenger. And Allah is Acquainted with what you do."
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صدق الله العلي العظيم
The verse 16:101 is the main ground to claim that God has cancelled some of his commands by replacing the new ones. This understanding comes from equating replacing with cancelling earlier commands which is not stated in the verse itself.
In fact, the verses of 16:101 and 2:106 themselves, are the best example of a potential case of abrogation. One may suggest the verse 16:101 states God might have substituted some verses with others while 2:106 emphasizes that God does not cancel a verse unless he brings in a better one or a similar verse. It therefore, appears that the verse 16:101 is replaced by 2:106.
The truth of the matter however, is the second verse of 2:106 is a clarification of the previous one. It is a further explanation of the same issue that God does not revoke an earlier verse but it provides a different perspective on the same matter to help us understand better or otherwise we are unable to find such a substitution in our memory which is the same as non-existence for us, humans.
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The first pair is viewed as referring to inheritance. It is believed that the verse 8:72 is meant to equally entitle the early immigrant believers, from Mecca, to what they would have obtained from wars or the Medina-based Muslims may have left after their death. In this view, the verse 33:6 cancels this equality in inheritance and limit the inheritance to relatives only, unless including them in inheritance is done voluntarily. I am not really sure how the verse 8:72 is associated to inheritance as the verse (in Arabic) clearly uses the word " ولایتهم " which has to do with protection not inheritance. That is to say, 8:72 is clearly stating that the newly established community in Medina does not have an obligation to go back to Mecca and fight for those few Muslims who didn't flee to Medina.
The verse 33:6 however, is prioritizing close relatives (= آرحام ) over all the other believers and Muslims in their entitlement ( possibly to inheritance). This verse is not talking about the obligation of protecting other Muslims if they seek help. Therefore, these two verses are clearly addressing two different concerns, thus the verse 33:6 is not abrogating the 8:72.
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The Second pair is said to determine the time when a widow should wait before she engages in a new relationship with another man. In this interpretation, the verse 2:240 specifies one year for the women before she can remarry. Accordingly, the verse 2;234 then reduces the wait period to four months and ten days only. This way, the verse 2;234 has cancelled an earlier command.
On a closer look on these two verses, we notice that the verse 2:240 is, in fact, commanding the men who are dying to support their wives for a year should their widow chooses not to leave the house of their dead man. This verse also emphasizes that if the woman chooses to leave their former husband's house before the end of the one year period, it is up to them and the husband is not be blamed for her decision to leave earlier than one year or why he didn't support her.
This is while the verse 2:234 addresses the widows (not the dying men), specifying their obligation to wait four months and ten days from their husband's death. After this period, they have the right to start a new relationships with another man if they wish to do so.
The important point in these two verses is although the dying husband has an obligation of providing for his wife for one year, the widow must only wait for four months and ten days to engages with another man. Needless to say, if the woman chooses to stay in his husband's house, which implies benefiting from his financial support, then she is entitled for one year on the condition that she does not take on a new relationship.
The fact of the matter is, I do not see any command being changed in these two verses. Each of the two verses addresses a different side of this relationship specifying two separate obligations. That is, the obligation of a husband to his wife after his death and the obligation of a widow to his former husband. There is no cancellation of an earlier command in this case either.
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The third pair is a perfect example of how the second verse provides further instructions following an earlier command (58:12) without conflicting it.The verse 58:12 is simply setting the requirement of giving a charity prior to consulting with the prophet. It also tells us that if you can't, God is forgiving, but it does not provide any alternative. The verse 58:13, on the other hand, is opening a way for those who have feared to give a charity. If they have sought God's forgiveness, they can pray and give "Zakat" which is a money to pay to the poor.
In other words, you may not be able to come up with a presentable charity when you are about to meet the prophet but you can make it up at your time with praying and giving a "Zakat" alternatively. Does the second verse ( 58:13) revoke anything in the previous verse? Absolutely and clearly not.
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Considering the above three pairs of verses that are said to be the most known cases in which an earlier command is abrogated by a new one, we can conclude that there is no such conflicting verses in the Quran or that we can not find them. I don't however, claim that I have checked all other cases and have refuted their potential contradiction as well. I am therefore, open to check any counter example you may find on this subject.