Speaking of Flügel's Quran. It had an effect on how the language of the Quran is studied and (mis)understood. Nöldeke (rightly) criticized Vollers for thinking the Flügel Quran was the 'standard text', and the qirāʾāt were non-standard variants. But confusion persisted, THREAD:
I've always been puzzled by this statement in Chaim Rabin's 'Ancient West Arabian' (1951). Rabin seems to suggest here that Ḥafṣ ʿan ʿĀṣim lacked the typical vowel harmony we find in textbook Classical Arabic, where -hu/ū and -hum are harmonized to hi/ī, -him. 
Now, I've read a good number of grammatical and qirāʾāt works on these pronouns, and I've never run into a claim that Ḥafṣ read without vowel harmony. It strikes me as extremely unlikely that al Suyūṭī (d. 911 AH) would be the first to mention it. So what happened here?
I couldn't get access to the 1904 edition of al-Suyūṭī's book that Rabin cites, but in a later edition the only time Ḥafṣ is cited is indeed in discussing the pronouns, so it seems safe to assume this is the same passage Rabin read.
Al-Suyūṭī says Hijazis lack vowel harmony, and Ḥafṣ read it in this manner, citing:
wa-mā ʾansā-nī-hu (Q18:63)
bi-mā ʿāhada ʿalay-hu ḷḷāh (Q48:10)
Upon reading this, Rabin supposedly looked up these cited passages in Flügel and did not find these unharmonized forms:
wa-mā ʾansā-nī-hu (Q18:63)
bi-mā ʿāhada ʿalay-hu ḷḷāh (Q48:10)
Upon reading this, Rabin supposedly looked up these cited passages in Flügel and did not find these unharmonized forms:
From this absence, it seems that Rabin concluded that al-Suyūṭī's statement was to be interpreted general statement: Ḥafṣ never had vowel harmony, unlike the classical pattern in the Flügel Quran, where it is always harmonized, leading to the puzzling statement in his work.
But had Rabin checked the Cairo Quran, or, in fact any Qirāʾāt work, he would've realized that these two examples were not to serve as examples of a general pattern but of specific exceptions to the rule. These two words are the only places where Ḥafṣ lacks harmony.
Rabin had access to the Cairo Quran, and cites double verse counts (Flügel count/standard Kufan count). It seems obvious that in this case he checked only Flügel.
Flügel's Quran in follows the reading of Ḥafṣ, but he seems to have "corrected" some forms he considered mistakes.
Flügel's Quran in follows the reading of Ḥafṣ, but he seems to have "corrected" some forms he considered mistakes.
This is not the only time that Flügel chose to get rid of features unique to Ḥafṣ. Ḥafṣ' famous dropping of hamzah in huzuwan and kufuwan (for huzuʾan and kufuʾan) is gone for example, rendering Sūrat al-ʾIḫlāṣ in accordance with every reading but that of Ḥafṣ.
As much as Nöldeke's criticism of Vollers gets cited, there are very few authors that seem to have actually understood the criticism. Most continue to operate with a (implicit) default assumption that there was a standard text, from which readers deviated.
This is wrong: the readings *are* the standard text. The weird linguistic features found there are not a random side note, they are an integral part of the Quran, and need to be integrated in our understanding of its language and its history.
I believe that the idea that the Quran was revealed in a language identical to what is prescribed in grammars like Fisher & Wright (something that is demonstrably wrong), is to a large extent the result of the academic inheritance of the confusion brought about by Flügel's Quran.
