There is no doubt that the meaning of episkopos by the time of the Pastorals had changed to regional superintendency.
The real question here is why anybody would wish to remove the Deuterocanonicals! The OT scripture in most common use in the earliest church was the Septuagint, the Greek translation of the OT, as is evident from the fact that two-thirds of NT references to the OT are indentifiable as references to the Septuagint. In particular, there are plenty of references in the NT to the Deuterocanonicals, which are simply part of the Septuagint. Of course the early fathers also happily cited from the Deuterocanonicals. It took until the Council in Florence 1451 until the dust finally settled on canoncity, but certainly the Deuterocanonicals were in the running from the start. Ben Sirach in particular was so popular in church readings that it got called liber ecclesiasticus "church book", or simply Ecclesiasticus.
Whether the Council of Jamnia/ Yavneh even existed is debated by scholars; there never was a "Council" of Yavneh IMO. Yavneh was, indeed, the place from which the Pharisees (also called Rabbis) ran the government of Palestine that had been entrusted to them by the Romans. Presumably some of their debates took place there also, possibly including the famous one about which of the hagiographa "render the hands unclean". But this was no "council". It was simply a lawyers' debate about the precise boundaries of a library that had already been established by usage. Note Joshua ben-Sira's grandson's phrase, "the law and the prophets and the other books of our fathers". Josephus too mentions the law, the prophets, and four other books which contain songs and precepts. It isn't certain what they were, but one plausible guess is Psalms, Proverbs, Song of Songs, and Ecclesiastes, these last two being the very ones about which doubts are raised in the Mishnah. So the Aramaic-speaking Jews of Palestine had one sacred library, established by custom, the Greek-speaking Jews of Egypt had another. The Qumran sectarians gave great respect to the Books of Jubilees and Enoch in addition, and seem to have disliked the book of Esther. But (so I understand) fragments of all the books of the Hebrew Scriptures except Esther have been found at Qumran, suggesting that the so-called "Hebrew canon" was already as stable as the Septuagint, and formed the sectarians' starting point. The Rabbinical debates about whether Ecclesiastes and the Song of Songs "soil the hands" may not even have been very seriously intended, though Akiba seems to have taken them seriously. Perhaps the lawyers were, as lawyers will, merely positing hypotheticals or raising iconoclastic questions for the fun of it.
Be that as it may, whatever Jamnia decided can in no way be considered binding on Christians. Jesus had passed His authority to the apostles, not to the Jewish priests and scribes. And it seems quite likely that however the Masoretic canon actually was arrived at, its final form may well have been influenced by the Jewish desire to combat that new sect Christianity. Why would Christians let their canon be dictated by those who oppose them?
So why did Martin Luther et al. kick out the Deuterocanonicals? Books like 2 Maccabees contain scriptural evidence for hated RC doctrines (in 2 Macc: prayers for the dead to free them from sin, merits of the martyrs, intercession of the saints). That's rather annoying if you are also propagating sola scriptura as a way of getting rid of the RC magisterium. So you construct some odd reason why against all history these books should be ignored (by adopting the Masoretic canon), and if that throws out old favorites like Ecclesiasticus, well, too bad.