Chapter 39, "Mesorah in Every Generation," elucidates, based on the Maharam Shick1 and Marganisa D’Rav,2 that the transmission of Torah (masores haTorah) is ultimately determined by the sages of each generation, grounded in the directive of 3 "וְאֶל הַשֹּׁפֵט אֲשֶׁר יִהְיֶה בַּיָּמִים הָהֵם - and to the judge who will be in those days" and the commandment of4 "לֹא תָסוּר - Do not deviate."
It follows that the kashrus of Sifrei Torah in any given generation is intrinsically bound to the mesorah upheld by Chazal of that era, irrespective of its precise alignment with the Sefer Torah originally transmitted by Moshe Rabbeinu.
A remarkable parallel may be drawn from an ostensibly unrelated area: the halachic examination of an animal's kashrus and the laws governing tereifos, injured animals.
Rashi and the Bahag
In the following passage, Rashi5 cites the Halachos Gedolos (Bahag) to the effect that our ability to halachically determine the kashrus of animals that suffered a serious injury has been lost. Notably, the precise language used by the Bahag mirrors that of the Amoraim6 in the context of masores haTorah: "ה"מ בדורות קמאי דהוו בקיאי למיבדק אבל אנן לא בקיאינן - This was true in earlier generations when they possessed the expertise to examine [the injured animal], but we are not experts." Rashi, however, takes issue with this position, invoking "וְאֶל הַשֹּׁפֵט אֲשֶׁר יִהְיֶה בַּיָּמִים הָהֵם" as the authoritative basis for applying the best available contemporary knowledge to determine the kashrus of such animals.
כתוב בהלכות גדולות כל היכא דבעי בדיקה כגון נפולה ושבורה ודרוסה דמיתכשרי בבדיקה ה"מ בדורות קמאי דהוו בקיאי למיבדק אבל אנן לא בקיאינן ולא סמכינן אנפשין
ולי נראה דאין לו לדיין אלא מה שעיניו רואות ומותר לסמוך עליו דכתיב (דברים יז) ואל השופט אשר יהיה בימים ההם אבל הוא יזהר יפה ולהביא לפניו כל הטבחים וכל הבקיאין בדבר כי היכי דנימטייה שיבא מכשורא:
It is written in the Halachos Gedolos: Wherever examination is required, such as in the cases of a nefula (an animal that fell), a shevura (a broken/injured animal), and a derusa (one attacked by a predator), which can be rendered permitted through examination, this was true in earlier generations when they possessed the expertise to examine [the injured animal], but we are not experts, and we do not rely on ourselves.
And it seems to me [Rashi] that a judge has only what his own eyes see, and he may rely on that, as it is written (Devarim 17): 'and to the judge who shall be in those days.' However, he should be careful and thorough, and bring before him all the butchers and all those expert in the matter, so that he may be aided by as many knowledgeable people as possible.
Mechaber and Rama
To further deepen the parallel, Chapter 46, "Reading from a Torah with Missing or Extra Letters," examines the divergent positions of the Mechaber and Rama7 regarding the discovery of a missing or extra letter during k'rias haTorah. Whereas the Mechaber draws no distinction between types of errors, the Rama rules that a Torah scroll defective solely on account of chaseiros and yeseiros does not require the removal of a second scroll.
As established in that chapter through an analysis of the Darkei Moshe,8 Chacham Tzvi,9 Pri Chadash,10 Maharitz,11 and Avnei Nezer,12 the crux of the dispute turns on the current state of masores haTorah and whether we remain in a condition of "אין אנו בקיאין - we are not experts." The Mechaber holds that the mesorah has been fully restored, whereas the Rama maintains that the Amoraim's declaration of "אין אנו בקיאין" remains operative.
This dispute finds a striking structural counterpart in hilchos tereifos. The Mechaber consistently rules in accordance with Rashi, affirming that the kashrus of an animal may be determined based on contemporary knowledge, while the Rama rules in accordance with the Bahag, maintaining that "אין אנו בקיאין" remains in effect.
Examples of this dispute are found in the following halachos in Yoreh De'ah: 18:6, 23:6, 24:6, 24:10 (see Biur HaGra), 33:6, 33:8, 55:10, 57:18, 58:6.
The following is one selected example:13
וושט אין לו בדיקה מבחוץ אצל דרוסה שצריכה בדיקה מפני שכיון שהוא אדום אין אודם הארס ניכר בו כיצד יעשה אם עוף הוא בודק הקנה מבחוץ [ושוחטו] ואח"כ מהפך הוושט ובודקו מבפנים ואם בהמה היא אין לה תקנה:
הגה ולדידן דאין אנו בקיאין בבדיקה אף עוף אין לו תקנה:
The esophagus cannot be examined from the outside in a case of derusa (one attacked by a predator) that requires examination, because since it is red, the redness of the venom is not noticeable on it. What should one do? If it is a bird, one examines the windpipe from the outside, [slaughters it,] and then turns the esophagus inside out and examines it from the inside. But if it is an animal, there is no remedy.
Rama: And according to us, since we are not expert in examination, even a bird has no remedy.
[Additional instances where the Rama disagrees with the Mechaber on the basis of "אין אנו בקיאין" are found in Yoreh De'ah 92:1 and 98:1 as well as Orach Chaim 317:1 and 330:5.]