What are the arguments against using manuscripts from the Cairo Geniza? Are there any Seforim / articles that discuss this debate?
There was an article in Tradition journal which discussed some of the arguments for and against using manuscripts in Halakha (which is what I'm assuming the questioner is looking for). It is linked here, but I'll summarize some of the main sources that would be relevant to dealing with this question (
While the position of the Mishkenos Yaakov is followed by the Aruch Hashulchan (O.C. 345:17), the Teshuvos Beis Efraim (O.C. 26-27) argues based on the aforementioned Urim VeTumim. Shulchan Aruch Harav, in his siddur, says that one should be strict regarding the sale of chametz because of new manuscripts of the Rishonim that have come to light that wouldn't have been considered by the earlier Achronim. Also on the side of using manuscripts we have R. Yaakov Ettlinger, (Shu"t Binyan Zion 69), who bases a ruling upon a newly discovered version of a Geonic teshuva. This also appears to be the opinion of the Mishna Berurah, as he approvingly cites the newly published Rabbeinu Chananel on Shabbos and uses it to argue upon the version cited by the Ran (Siman 340, Biur Halacha 'bein beyad'). It should be noted, however, that in almost all of the above cases, manuscript evidence was used to rule strictly, not leniently.
The Chazon Ish (Letters vol. III no. 48) says that because the Shulchan Aruch was not actually based solely on the majority rule between the Rambam, Rif, and Rosh (despite its author's introduction), we can't use manuscripts to argue on the Shulchan Aruch, which was accepted anyway. Furthermore, he implies (Eiruvin 67:12) that we shouldn't rely on the newly published Rabbeinu Chananel because, as it hasn't been in use for centuries could therefore contain serious typographical errors. (This observation is also noted by the Seridei Eish in several places as well). In Letters of the Chazon Ish (vol. I no. 32) he also seems angry that someone should try to answer a question in the Gemara based on textual variations, and in vol. 3. letter 2, he clarifies that this is because the accepted version of the Gemara is due to divine providence.
Similarly, R. Moshe Feinstein would dismiss newly discovered writings that ran contrary to his opinion (see Iggeros Moshe E.H. vol. 1 63:6, Y.D. II:7 and Y.D. III:14, plus more).
A further issue is where a manuscript was discovered from an author who isn't known to us as a talmid chacham. R. Ben Zion Uziel writes (Choshen Mishpat, Tinyana 6:2) that we follow Rishonim because of their personal greatness, not the era in which they happened to have lived, and so just because a work is old doesn't make it reliable.
Aside from one or two extra sources, all of this came from the article linked above: Moshe Bliech, "The Role of Manuscripts in Halakhic Decision Making: Hazon Ish, his Predecessors and Contemporaries", Tradition 27:2 (Winter 1993)
There is a similar question relating to the writings of Rabbi Menachem Meiri and would seem to be equally applicable to the question of the Cairo Geniza: Quoting wikipedia: