Dear Dovid,

I'm really very sorry for taking so long to reply -- I'll bet you never expected to see this question again! In fact, I myself was bothered terribly by that very question when I learned the Sugya, and was not able to resolve it in time for the publication of our Insights. Rav Gidal must be teaching something about Kodshei Kodshim as well as Kodshim Kalim, as the Gemara makes clear at the end of 5a. (I didn't see anybody who so much as mentions the question, although I looked high and low.) Unfortunately, I had already begun Nidah by the time I received your question, and was not free to go over the Sugya in depth at the time. On Pesach, I finally reviewed the Sugya, and I believe that I now can answer your question.

(a) One is Mo'el on the flesh or the Eimurim of Kodshei Kodshim until the Zerikah, after which point one is only Mo'el on its Eimurim

(b) Therefore, there are 2 ways to remove the prohibition of Me'ilah from Kodshei Kodshim: (1) Through a kosher Zerikah, Me'ilah is removed from the flesh of the animal, as I stated in (a) -- this is the subject of Rav Gidal's discussion, Me'ilah of the flesh of Kodshei Kodshim; (2) If the animal died, since "Kodshim she'Mesu Yatz'u m'Yedei Me'ilasam", Me'ilah is removed from the Eimurim as well as the flesh.

(c) Your question may now be answered. When our Mishnah says that the prohibition of Me'ilah remains when an animal is slaughtered with Machsheves Pigul, it is referring to the Me'ilas Eimurim . Even though one is normally Mo'el on Eimurim even after a kosher Zerikah, one might have thought that after an invalid Shechitah/Zerikah one is not, because of (b:2).

(d) However, this explanation will only suffice according to Rashi's interpretation of the Gemara on Daf 2a. Tosfos (ibid. DH Chutz), however, takes a different approach, saying that the Mishnah is teaching that Pigul is not considered the equivalent of a kosher Shechitah/Zerikah (since Pigul is always equated to "Hartza'as Kosher"). It would seem from Tosfos that the Mishnah indeed states explicitly that Machsheves Pigul does not remove Me'ilah from the flesh of Kodshei Kodshim like a kosher Zerikah does, which is exactly what Rav Gidal is discussing! (The Mishnah cannot be discussing the status of the Eimurim; there is no reason for any kosher Shechitah/Zerikah to affect the status of the Eimurim, as above, b:1!)

(e) In truth, though, when one carefully analyzes the subject it is clear that Tosfos is indeed referring to Me'ilah of the Eimurim, and not the flesh. The reason that a kosher Shechitah, in this case, would remove Me'ilah from the Eimurim is because of "Na'aseh Mitzvaso," that is, because all that the Torah requires to be done to this Korban was already done to it. No more is required of us (since obviously we cannot offer Pigul on the Mizbe'ach). Also, such a Korban cannot be called "Kodshei Hash-m" (as Eimurim of a normal Korban, which must be offered on the Mizbe'ach), a defining factor in the prohibition of Me'ilah, since it is no longer to be used by Kodesh at all. This is why the Machsheves Pigul might have removed Me'ilah from the Eimurim of Kodshei Kodshim, had the Mishnah not explicitly told us that there is Me'ilas Eimurim.

The Mishnah does not discuss the status of the flesh at all. It is possible that the Zerikah removed Me'ilah from the flesh (since it is like a kosher Zerikah), and it is also possible that it did not (since it is Pigul, after all). Rav Gidal is therefore justified in questioning the status of the flesh in a Korban Pigul with regard to Me'ilah.

Be well,

-Mordecai