Alleged Contradictions in the Qur'an answer

Confirming the Old Revelation or Substituting it
The new revelation confirms the old [2:97] or substitutes it [16:101]?
Verses in question:
2:97. Say: "Whoever is an enemy to Jibrael (Gabriel) (let him die in his fury), for indeed he has brought it (this Qur'ân) down to your heart by Allah's Permission, confirming what came before it, as guidance and glad tidings for the believers.

16:101. And when We change a Verse in place of another, and Allâh knows the best of what He sends down, they (the disbelievers) say: "You (O Muhammad ) are but a forger!" Nay, but most of them know not.

The truth of the matter is that these two verses describe two totally seperate issues with regards to God's revelation. Verse 2:97 describes the fact that the Qur'an confirms the revelations delivered to previous nations, while verse 16:101 describes the Qur'anic concept of abrogation. The following points clarify these two issues:

1. With regards to verse 2:97, Syed Qutb (d. 1966CE) writes the following in his prominent Fi Dhilalil Qur'an:

The Qur'an was lodged in Muhammad's heart, confirming "
the Scriptures revealed before it, and is a guidance and joyful tidings for the believers".
The Qur'an confirms and endorses in general terms all Divine revelations recieved before it. The religion of God, as expounded and preached by all revealed Scriptures, is basically one and the same. All Divine revelations have come as guidance to man and as a source of joyful tidings for all believing hearts that are receptive and willing to have faith in God.(Qutb, In the Shade of the Qur'an, The Islamic Foundation 1999, vol. 1, p.95)
And Shaykh Abu Ammaar Yasir Qadhi writes:
However, as a manifestation of Allaah's mercy, mankind was not left without guidance in its social and political life. Rather, their Creator provided for them a set of laws that would govern them in their mutual affairs, and instruct them concerning all that was beneficial for them, and warn against all that was harmful to them. These code of laws varied from time to time, and from place to place, for each set of peoples had their own specific problems and peculiar situations that needed to be catered to. Allaah says,
And for every nation, We appointed (their) religious ceremonies, so that they may mention the Name of Allaah...[3:50]
Since each prophet was sent to a different nation, it was possible for one messenger to abrogate the laws of a previous messenger. (Qadhi, An Introduction to the Sciences of the Qur'aan, Al-Hidaayah Publishing and Distribution 1999, p. 245)
Thus, the Qur'an confirms the laws, beliefs and stories found in previous scritures while it also serves as a criterion in identifying false notions and doctrines which have crept into previous scriptures through corruption. Although the Qur'an confirms the message of the previous revelations it also contains some different laws which are more appropriate for the Muslim nation than older laws such as the Mosaic laws. As Moiz Amjad comments:
Mr. Katz contends that the Qur'an cannot confirm as well as substitute the previous scriptures at the same time. The reason for this contention is that Mr. Katz has taken the word 'confirm' to imply 'to approve, to sanction or to endorse'. The word, however, is also used to mean: 'to verify, to prove and to certify'. Mr. Katz is correct in contending that the Qur'an cannot "confirm" (i.e. approve/sanction/endorse) the old scriptures as well as substitute or abrogate them. However, I am sure all would agree that there would be no contradiction in saying that 'even though the Christians "confirm" (i.e. verify/certify) circumcision to be a part of divine law, yet consider the obligatory nature of this law to be abrogated.' In the same way, there is obviously no contradiction in the statement that "the Qur'an, on the one hand "confirms" the divine origin of the previous scriptures, and on the other, substitutes its laws with the new laws".
The Qur'an only confirms the message of the previous revelations in their original form, not the tampered form that has survived. As for the tampered form, then the Qur'an confirms what is correct and distinguishes it from what is false. Furthermore, some of the details in the laws of previous revelations were particular for their respective nation, and consequently the Qur'an contains laws that are more appropriate for the followers of Prophet Muhammad (peace be upon him).

2. With regards to verse 16:101, then this explains the concept of abrogation (naskh) in the Qur'an. The Qur'an was revealed gradually to the Prophet Muhammad (peace be upon him) allowing his followers to gradually becoming stronger in faith and able to follow the laws of Islam. As Shaykh Abu Ammaar Yasir Qadhi mentions:
Among the blessings of Allaah to the Companions is that He revealed to them the laws of Islaam gradually, and thus made it easier for them to adopt these laws. Initially, there were no specific laws of halaal and haraam. The Companions during the Makkan stage were being trained spiritually so that they could form the nucleus of the future Muslim state in Madeenah. Once they had passed this stage, Allaah then completed the revelation of the sharee'ah in gradual steps, so that they could adapt to the lifestyle of Islaam.(Qadhi, An Introduction to the Sciences of the Qur'aan, Al-Hidaayah Publishing and Distribution 1999, p. 86)
Thus, early Qur'anic verses may have contained a general or light directive which was later substituted for a specific ruling laying down a concrete law. For instance, the Qur'an initially stated that there was much harm and some benefit in alcohol (2:219) after which many Muslims began to abstain from alcohol more. Then the Qur'an forbade the believers to perform prayer when intoxicated (4:43) and later on it declared alcohol to be categorically forbidden (5:90). In this manner, the Qur'an gradually revealed laws through a process of substituting a few verses, which aided in establishing the Islamic practices. Had alcohol been forbidden at once in a society where it was a firmly-rooted practice, the message would have been too difficult to follow. Abrogation does not imply any imperfection on the part of God, as some crtics claim. It only illustrates the changing condition of society and the need to provide laws relevant to a nation's context in the world. For more information on Abrogation,

To conclude, verse 2:97 indicates that the Qur'an confirms the truth found in previous scriptures while verse 16:101 describes the gradual revelation of Islamic law and how one verse is exchanged for another. Thus, there is no contradiction between the two.