Rebbi Shimon's Opinion #1: 'Whereas according to Rebbi Shimon, this is not considered prepared'.

Rebbi Shimon's Opinion #1 (cont.): This cannot mean that it is not prepared, because it is Muktzah - since Rebbi Shimon does not hold of Muktzah.

Rebbi Shimon's Opinion #1 (cont.): What the Gemara therefore means is that wherever the blemish is not known (when Yom-Tov comes in), in that a Chacham did not examine it before Yom-Tov, so that it was not known whether the blemish was a permanent one 'it is not prepared' - meaning that the Heter is not permitted, i.e. it is not prepared to become permitted, since one is not allowed to examine blemishes on Yom-Tov.

Rebbi Shimon's Opinion #1 (concl.): Either because it resembles repairing, or because it is like Paskening a Din, both of which are Asur mi'de'Rabbanan. This is how Rashi explains it.

Refutation #1: Firstly, 'This is not prepared' implies that even if a Chacham does examine it, seeing as it was not known before Yom-Tov that it was a permanent blemish, Rebbi Shimon forbids it.

Refutation #1 (cont.): Whereas according to Rashi, it implies that it is only not prepared Lechatchilah, but that Bedi'eved, it is permitted?

Refutation #2: Secondly, the Gemara in Perek Kirah (Shabbos, Daf 46:) clearly indicates that Rebbi Shimon forbids it on account of Muktzah ...

Refutation #2 (cont.): Since the Gemara asks how Rebbi Shimon holds here of Muktzah, when we know that in general, he does not hold of Muktzah?

Rebbi Shimon's Opinion #2: Tosfos therefore concludes that Rebbi Shimon means that it is Muktzah, since it is not prepared, and that even if one transgressed and did examine it, it remains Asur because of Muktzah.

Rebbi Shimon's Opinion #2: In fact, they argue over whether one is permitted to examine blemishes, and based on the extra words 'This is not prepared!', concerning Muktzah too.

Clarification #1: And when the Gemara asks here 'Let them argue just over examining blemishes?', it means where the animal did not fall into a pit, like the Lashon of the Mishnah of Muktzah?

Clarification #2: And similarly when the Gemara says 'We might have thought that, since his mind is on it, one should be permitted to Shecht it; therefore it comes to teach us ... '. This means that is forbidden on account of Muktzah, and that even if one did inspect it Bedi'eved, it is Asur, even according to Rebbi Yehudah, since it did not have a permanent blemish on Erev Yom-Tov.

Clarification #2 (cont.): Whereas, according to Rebbi Shimon it is forbidden even if it did have a permanent blemish, because it is Muktzah, as we explained, not like Ada bar Uchmi (on Amud Beis).

Question: Why is this case different than everywhere else, where Rebbi Yehudah is more stringent with regard to Muktzah than Rebbi Shimon?

Answer: There is good reason for this - because, seeing as he permits examining a blemish on Yom-Tov, and it was known before Yom-Tov that the animal had a permanent blemish, it is therefore not Muktzah, since his mind was on it since yesterday.

Answer (concl.): Whereas according to Rebbi Shimon, who forbids examining a blemish on Yom-Tov, his mind was therefore not on it from yesterday. Consequently, it is forbidden, even if he did examine it.

Explanation #1: Because Rebbi Yehudah ha'Nasi does not hold of Muktzah, since he says that if it has a permanent blemish, even if it occurred on Yom-Tov, one may haul it up and Shecht it; and these Tana'im do not hold of Muktzah by a B'chor, since the owner's mind is on it - in the hope that a blemish will occur.

Explanation #1 (cont.): 'And if not' - that it is not blemished, 'one may not Shecht it'.

Question: Why is this not obvious, seeing as it is a Tam?

Answer: One may not bring it up by means of a trick Shechitah (like Rebbi Yehoshua), as the Gemara explained above.

Implied Question: The Gemara did not want to give this answer according to Rebbi Yehudah in the Mishnah ...

Answer: Because it did not want to give a Dochek answer, to say that one may not haul it up by means of a trick Shechitah ...

Answer (cont.): Since it has another answer - that Rebbi Yehudah holds of Muktzah by B'chor, it is therefore forced to establish it by a Ba'l-Mum.

Answer (concl.): Whereas Rebbi Yehudah ha'Nasi, who does not hold of Muktzah by B'chor, since he is talking about a Tam that fell into a pit, it is not possible to give the same answer - 'that a permanent blemish occurred on Yom-Tov', like the Gemara answered according to Rebbi Yehudah in our Mishnah.

Explanation #2: In a second explanation, Rashi omits the word 'Tam' from the Beraisa, so that it reads 'A B'chor that fell into a pit, if it has a permanent blemish which was known before Yom-Tov, one may Shecht it ...

Explanation #2 (cont.): And if not, only the blemish occurred on Yom-Tov, one may not Shecht it' - even if one hauled it up, because it is Muktzah. And Rebbi Yehudah ha'Nasi does hold of Muktzah.

Implied Question: The Gemara did not ask, as it did on Rebbi Yehudah in the Mishnah 'Why is it not obvious, seeing as it is Muktzah'?

Answer: Because, whereas according to Rebbi Yehudah in our Mishnah the question is justified, because why does it need to teach us this? If it is to teach us Muktzah, we know from from many other sources that Rebbi Yehudah holds of Muktzah.

Answer (cont.): Whereas regarding Rebbi Yehudah ha'Nasi, the Tana needs to inform us that he holds of Muktzah.

Question: Later in the Masechta (Daf 40.) We are uncertain as to whether Rebbi Yehudah ha'Nasi holds of Muktzah or not. Why does it not resolve the She'eilah from here?

Answer: The Gemara cannot resolve it from here, since there two versions of Rebbi's opinion, as we just explained, one of which holds of Muktzah and one of which doesn't.

Answer (cont.): And the Gemara's uncertainty is based on which is the correct version.

Conclusion: That is why the Gemara there could not possibly bring a proof from here (See also Tosfos, Shabbos, 45: DH 'li'Devarav').