1.

a. The Kesef Mishneh (written by Rav Yosef Karo, the author of Shulchan Aruch) on the Rambam (Hilchos Bi'as ha'Mikdash 7:7) gives an interesting explanation for the Mishnah (40a) which may help answer your question. He writes that the first Beis Din did not dispute Ila's ruling totally, but rather they merely said that they had not heard about the three Mumim that Ila added. This Beis Din did not agree with Ila, but on the other hand did not argue with him either.

b. The Kesef Mishneh uses the principle stated elsewhere in the Gemara (see Kesubos 23a) that "Lo Ra'inu Eino Ra'ayah" -- if one asserts that such a thing has not been seen, this does not prove that it does not exist. The Kesef Mishneh writes that in our case, "Ein Lo Shamanu Ra'ayah" -- the mere fact that the first Beis Din said that they had not heard about the three Mumim of Ila does not prove that they are not actual Mumim.

c. According to this approach, the second Beis Din is not saying directly that the first Beis Din was wrong, but rather that it is more expert than the first Beis Din on questions concerning Mumim. That is, while the first Beis Din did not know that these three are Mumim, the second Beis Din did know. This is partly because the second Beis Din agreed with Ila who was a great expert in these matters.

d. One does not have to say that until then, Ba'alei Mumim were slaughtered in the Beis ha'Mikdash, because, first, it is possible that no practical cases of Ila's three Mumim actually occurred in the times of the first Beis Din, and, second, and even if cases did come up, the first Beis Din perhaps did not permit them to be slaughtered because they themselves were not sure that they were considered Mumim.

2. Even if we do not use the above explanation of the Kesef Mishneh, but instead we explain that the first Beis Din did issue a definite ruling, we still can understand the change of direction on the part of the Beis Din. There is a principle that every ruling that the Beis Din of its generation issues is binding for those times. The source for this is the Gemara in Rosh Hashanah (25a). There, the Mishnah relates a case in which there was a major dispute about when the New Moon occurred. Raban Gamliel issued a controversial ruling. The Mishnah states that since Rabban Gamliel was the head of the recognized Beis Din, his ruling was authoritative; if we would question the ruling of Raban Gamliel, then we would have to question the ruling of every Beis Din all the way back to the time of Moshe Rabeinu. Accordingly, here in Bechoros, the ruling of the first Beis Din was authoritative in its time, and therefore it determined the Halachah in that generation. However, later on, a second Beis Din was able to change the ruling of the first Beis Din. The Gemara in Megilah (2a) states that a Beis Din cannot cancel the ruling of a previous Beis Din unless it is greater than the first either in wisdom or in numbers of judges on the Beis Din. In our case, the second Beis Din was more expert in the Halachos of Bechoros than the first. This was because Ila was on the side of the second Beis Din. Since Ila was such a great expert in the Halachos of Bechoros, his support meant that the majority of judges retracted from their original opinion and now held that all three of Ila's new Mumim were indeed Mumim to allow the slaughter of the Bechor. This does not mean that until that time Bechoros Ba'alei Mum were sacrificed on the Mizbeach because until that time they were not considered Ba'alei Mum. It was only when the second Beis Din changed its ruling that they became considered Ba'alei Mum.

Kol Tuv,

Dovid Bloom