Brother Shakeeb replied to this video in detail on request. I am posting his response below:
"To be honest with you, I don't think myself to be capable of framing a scholarly response. So if you find any scholarly response, please feel free to share it with me too! But nevertheless, I do have a personal perspective on things which I will share with you. Fortunately, none of the claims made in the video are erudite enough to require detailed citations from classic text. Here it goes:
1) The genius who made this video and perhaps the researcher himself (based on how he is presented) is unaware of the fact that the books written on Uloom ul Quran by Muslim scholars already mention that the first generation of manuscripts used to be written without any dots, a'rabs and punctuations. The only thing startling here, if it must be put that way, is that his discovery (pun intended) corroborates the consistent account of Muslim historians about the development of Quranic print throughout.
2) Then he is concerned that it leads to 5 possible identities of the words. What he conveniently forgets here is the oral tradition of Quran which spread at a far greater scale in parallel with the written manuscript simply because it was an era preceding the invention of press. He seems to be under the delusion that just like our times when we simply lend over a book to someone to read, back in those days Quran also used to be handed over to people to read and figure. The fact, however, is that from the very beginning to-date there always has existed this very strong culture of having full-fledged schools and study circles for teaching Quran organized by scholars who had learned it directly from their previous generation until companions of the prophet. It is not without any reason why the second caliph Umar had sent one of his very close aides and foremost scholars of Quran Abdullah bin Masood to Kufah for institutionalizing the teaching of Quran there. Written text in the beginning could only mean to correct any lapses appearing in the memorized part and not to be used as the sole source of information on Quran. In fact, this trend has lasted even today in the sense that people rather than understanding Quran completely on their own prefer to study it at least with the help of a brief Tafseer (now that there is no more ambiguity in the rules of writing) if not directly from a teacher. This process of learning from people who learned it in their turn most likely from the close companions of the prophets ensured that the imagined possibility of five different words in one place never materialized at least to a sustainable level. Those guys who wrote the script knew about its shortcomings as well as us now and it is quite arrogant to completely ignore the aforesaid method of teaching the book and insinuate that their was no mechanism in place to guard against its weaknesses.
But for the sake of argument, let us assume that teaching Quran by the scholars in parallel with distributing the transcript was inadequate and the early generations were indeed confused into having five separate readings of Quranic verses on average (yes, not five different versions of the whole text!). As a consequence, there must have been diverse narrations of Quran at least found in geographically dislocate regions much larger in numbers than the diversity found in the narration of a particular incidence in Ahadeeth (although it is due to different reasons altogether.) And this diversity should have then remained in the versions of Quran compiled by the later generations as well. What we see here, however, is an astounding unanimity over the identity of the text accepted by Islamic scholarship as well as masses from Arabian peninsula itself to far eastern countries in the Africa to Spain in the west. Mind you, I am not denying mistakes made by lay people and possibly by individual experts which are not uncommon in our times too despite the availability of Quran in black and white. But do the community at large begin to take an individual's or even publisher's mistake for the confusion in the correct version of Quran? Or all these isolated aberrations die out in the process of mass-transmission from one generation to another?
If that is not enough, then consider two further scenarios. Just like there are various sects and schools of thoughts based on disagreements over the interpretation of Quran as well as the acceptance of different traditions of hadeeth, there must have been far major differences over the acceptance of various identities of the words in Quranic text itself. It should not take a genius to figure that a disagreement of this kind over the reading of Quran would lead to fissures in various strains of Islamic scholarship far greater in magnitude than what could ever arise due to differences in the interpretation of the text or Hadeeth literature. But where is it? If not, what does this imply? The next curious point is to remember that Quran used to serve as the fundamental basis of Islamic law from the very beginning of Islamic state in Medina until the pre-colonial era. Since we are asked to believe that in the early days there was a great deal of ambiguity in the reading of Quran, we should understand as a natural corollary an extreme chaos in the functioning of the legal system of Islamic state. To imagine what I mean, just think of Pakistan's penal code used in our courts with the same level of uncertainty in the identity of the words in addition to the interpretation which is quite natural. It is trivial to visualize the utter dysfunctional-ization of any legal infrastructure this will necessarily lead to. And so if it did happen to the practice of Islamic law, how did everything converge to just one word instead of five or even more? Again, why weren't there any disagreements? How did muslim historians manage to mention the lack of punctuations, dots and a'rabs in the early manuscripts which amusingly he is discovering in the twentieth century but wrote off the consequences? Again, why did it not lead to differences in juristic schools? Why? Why?!
As this guy is challenging a well established historical narrative, it is his responsibility to explain away existing realities by filling up all the gaping holes which appear as natural corollaries of his narrative as I pointed above. For starter, he should explain when five different identities of wrods were possible, how come only one survived? What made a society as huge as that to agree on one reading? How can an event as massive as the convergence to a single word fail to find seat in histories written by any sect in Islam whatsoever?
And nobody here can counter it by citing disagreements about the completeness of Quranic text as it is purportedly claimed by minor/major groups in shiite tradition. For one, even shia theologians both past and present almost completely, if not absolutely, abandoned this position. For another, it was about certain portions of Quran failing to find their place in the widely accepted manuscript. It was never a dispute about choosing one of the five possible words written in the text.
Before leaving, I should point out here the issue of seven "qira'at" of Quran which is a well discussed topic in the Islamic scholarship. Since he is claiming something unknown here, I believe his work does not relate to that either and hence we don't need to talk about it.
3) It yet again makes a disappointing case for a ground-breaking discovery that the newly-found text of Quran was overwritten on something else. Why is it so surprising? Why cannot the same parchment, leaves, bones or whatever form of paper in vogue at that time be reused for something else? Please, why is it so significantly surprising at all? As it can very well be a personal copy of a student, instructor or any common man for that matter, why can't it even include some personal notes scribbled in between? Why can't we get real for a while?
4) This last point takes the cream. The guy who made this video could not have been more ignorant of his own ignorance. He presumes that the differences in translations are somehow explainable by this so-called discovery. It is amusing how he digs out from oblivion an unknown researcher in Germany (?) but didn't bother to check out with someone familiar with Quran's translations to inquire about the apparent diversity. Ignoring all the general liguistic issues in translating a literary work from one language to another, Arabic language itself allows for multiple meanings (not identities) of the words placed in one sentence. On occasions, some of these meanings are all plausible simulataneously while at others only one or two can be valid given the overall context of the discourse. This leads to differences in understanding which sometimes find its way into the translations too. It has got nothing to do with any ambiguity about the identity of words themselves."
In the end, i just like to say what Quran says: they want to destroy the noor (light) of Allah with their breaths, uttering only falsehood...