In Part 1, we have seen how Rodwell thinks that Quran arrangement is gibberish, and he sets out to correct it. In Part 2, we have seen how Jeffrey attempts to discredit the authenticity of the Quran that we presently have, claiming that it has been tempered like other scriptures.
In this part, we shall try to understand what exactly they are trying to do, what might be their motives, and how these relate to surahs al Mu’awwidhatayn.
Let’s try to uncover their motive first. One Internet site by the name answering-islam.org seems to provide at least some of the clues.
On the topic, Contradictions in the Quran, the opening paragraph of the above site says:
We do not reject the Qur'an because of this list of contradictions. There are many reasons of much more substantial nature why we do not believe the Qur'an to be from the one true God... This page is not intended as an attack on the Qur'an. Sadly, many Muslims have become unnecessarily aggravated because they did not understand the purpose of this collection.
Sounds good so far, but the author of the above article (who wish to remain anonymous) does have an issue with the Muslims. He says:
Muslim web sites abound in articles and collections attacking the integrity of the Bible by means of contradiction lists. Many have the attitude that "because the Bible is riddled with contradictions, errors, absurdities and problems, there is no need for me to make the effort to understand it." With such an attitude no real dialog can develop.
Now we know what is the issue. The above author does not like our "attitude." He then proceeds by delineating the problems that he has with this “attitude,” which for the sake of brevity, need not be quoted. The author then continues:
If both sides can come to the recognition that their own book, the scripture which is the basis of their faith, be it the Bible or the Qur'an, contains some very difficult passages which might even look like plain errors or logical contradictions (depending on the level of hostility employed when looking at it), then we might be more forgiving towards the other and be motivated to not judge prematurely but to make a serious effort to understand each of the books and the essential teachings of the respective faith in a deeper way before we come to a decision why we do or do not believe them. (1)
Ah, it is not really about our "attitude" then. The bone of contention is our refusal to recognize our Holy Scripture to be flawed, just like theirs.
But anyone who is familiar with the Bible Study would know that the Bible has been proven NOT to be the words of God. The Christian scholars have already admitted as much. They still believe Bible to be the words of God, though, but not the exact words of God, for the Bible has been tempered with scribal errors over time. In other words, they believe the meaning and the intent of the Bible are what God has intended, although its words are not exactly His.
The above author is irritated and incensed because, not only that the Muslims refuse to recognize that the passages in Bible are indeed what God has intended, although its wordings may not have been exactly how God has worded them, but the Muslims are also adamant in claiming that their Quran contains the exact Words of God, has not been tempered with, and without any contradiction whatsoever.
It sounds more like being envious, is it not?
Since the Bible has been tempered with, and there is no way they can prove that it contains the genuine words of Gods, much less to correct it, because the Original has been lost, the Quran too, must be the same. Any claim to the contrary only shows that the Muslims are incorrigible, arrogant, and incapable of admitting that the Quran too has been tempered with human errors, though none of these is done with ill intention.
If we ponder about it, we must say that they have every reason to be envious. They know that they cannot claim the words in their Scripture to be authentic, exactly as revealed by God Himself, but we can. And they have admitted that their Scripture has been tempered with during the compilation, but we have no ground to admit as such, because we know that the Quran has been preserved as it should have been preserved, the way God has intended. Since they are humble enough to admit scribal or whatever errors have crept into their Scripture, they are quick to label us as being arrogant when we insist that our Quran contains no error.
It is this envy that has led them to attempt to discredit Islam by reducing Quran to the status of their Bible in the most subtle way. In the process, they have managed to gain some influence among the so-called Muslims, which is why Allah asks us to seek refuge with Him so as to be protected from their envy and their conspiracy.
Which is what al Mu’awwidhatayn is all about.
In al Falaq, Surah 113, Allah says:
Say: "I seek refuge in the Lord of Daybreak,  From the evil of that which He created;  From the evil of the darkness when it is intense,  And from the evil of the witchcrafts when they blow in the knots,  And from the evil of the envier when he envies.” 
In an Nas, Surah 114, Allah says
Say, “I seek refuge with the Lord of mankind,  The King of mankind,  The God of mankind,  From the evil of the whisperer who withdraws,  The one who whispers in the hearts of mankind,  From among the Jinn or Mankind.” 
Surah al Falaq is about seeking protection from the witchcraft or from the envier who envies. In practice, these two are generally inseparable. The witchcraft is usually performed by a witchdoctor upon the request from the envier who envies with what his friends, adversaries or competitors have.
As we know, the black magic works on mind and perception, which has the effect on the body. In the surah above, they recite whatever mantra required and blow in the knots, pretty much like the witchcraft or voodoo as currently performed. The Surah asks us to seek refuge from this evil by reciting it.
As al Mu’awwidhatayn are said to be revealed together, there is a remarkable connection between these two surahs as far as our current observation is concerned.
While Surah al Falaq talks about the black magic, Surah an Nas talks about the “white magic.” The “white magic” in question is the Arabic word “waswas”, translated as “whisper” in Verse 5 above. “Waswas” of course is not “white magic.” It is generally translated as “whisper” or “conspire” with the intent to create doubt, but its effect has been magical, as we shall see shortly.
The Malays also use this word in their vocabularies, but with a very confined meaning. When they are not sure whether something has already been done, or already happened, or in fact hasn’t, then they are in the state of doubt. This state of doubt is called “waswas.” For instance, they are being “waswas” (in the state of doubt) about the number of cycles in their prayer, whether they have performed three or four cycles already. And they attribute this forgetfulness to the “whisper” of the Devil who put doubts into their hearts.
This is one meaning of “waswas,” but a very confined one. The harm in that is minimal, and concerns mostly an individual. A more harmful “waswas” is the active effort of creating doubt in the hearts and minds of the Muslims by the Orientalists and the enemies of Islam. Among such works are the ones made by Rodwell, as we have seen in Part 1, and Jeffrey, in Part 2, of this series.
While the crafts employed by Rodwell and Jeffrey do not involve blowing the knots, they still use the mantra, either spoken or in writing, with the intent to blow the mind and create a set of perceptions which eventually lead to certain type of behaviour.
What motivates them to do this would be anyone’s guess, but envy is definitely one of the reasons. Since their scriptures cannot be proven to be the actual Words of God, then might as well make the Holy Scripture of Islam to be tempered with human errors as well. Since Christianity has been successfully secularized after the Renaissance, then might as well secularize Islam as well, as their kinds have been doing with much success for the last few centuries.
Their “white magic” has succeeded in confining Islam to a mere set of beliefs or rituals. Their works have succeeded in desanctifying and secularizing the daily life of the Muslims, which should have been governed by Syariah or Islamic Law. Many portions of the Words of Gods and the Prophetic Traditions that govern the laws of their daily lives are abandoned, on the pretext that these are unsuitable to the modern times.
That, at least, is the impression one can gather from Surah al Falaq and an Nas combined together.
We can seek refuge from the effect of the black magic by reciting Surah al Falaq. We can also seek refuge from the effect of temporary doubt and forgetfulness (ordinary “waswas”) by reciting an Nas. The harmful effects of “white magic,” devised by those who are envious and hostile to Islam, can only be sought by understanding the inherent meaning of these two surahs. A mere recitation of them would bring no desired result.
Incidentally, among the famous arguments made by these whisperers is that al Mu’awwidhatayn are not part of the Quran. They are just invocations to seek refuge, as we have mentioned in the IntroductoryRemarks. But they mention only one part of the story. It seems that there are spurious reports containing Ibn Mas’ud’s allegation, that Surah al Falaq and Surah an Nas are not part of the Quran. What they do not tell is that the same spurious reports also indicated that Ibn Mas’ud had made an error, and later repented, as Sayyid Qutb explains in his famous commentary. Al Azami devotes a whole chapter on this issue in his book, The History of the Quranic Text: from Revelation to Compilation, in case you are interested in the subject.
This concludes our remarks and observations on al Mu’awwidhatayn as well as the series of the Four Quls.
Quotations above taken from: http://answering-islam.org/Quran/Contra/