Gemara

(Mishnah - Shamai): A woman who sees that she became a Nidah is not Teme'ah retroactively;

Hillel says, she is retroactively Teme'ah from her last Bedikah (when she checked herself).

Question: Why is a Nidah different than something immersed in a (possibly deficient) Mikveh?

(Mishnah): If something Tamei was immersed in a Mikveh (which used to be full) that was later measured and found to be deficient, and later it touched Taharos, whether it touched in a Reshus ha'Rabim or Reshus ha'Yachid, it was Metamei them.

Answer #1: The first entity is considered Vadai Tamei, for it had this Chazakah. Perhaps the immersion was invalid.

Objection: The Mikveh should retain its Chazakah, that it was full (at the time of immersion, so the immersion was valid)!

Answer #2: A Nidah has only one Re'usa (reason for concern, i.e. she sees blood now). Regarding the Taharos there are two (the Chezkas Tum'ah of what was immersed, and the Mikveh is deficient now).

Kidushin 66b (Beraisa - R. Tarfon): If a Mikveh was once known to be full, and it was found to be deficient, we are not Metamei anything Tamei that was immersed in the Mikveh.

2. R. Akiva says, it is Tamei.

R. Tarfon: This is like a Kohen who was offering Korbanos, and it became known that he was a Chalal (born to a divorcee). What he offered is acceptable.

R. Akiva: No, it is like a Kohen who was offering, and it became known that he has a Mum (blemish). What he offered is not acceptable. One witness can testify about a deficient Mikveh or a Mum, but two witnesses are needed to testify that a Kohen is a Chalal;

Also, a deficient Mikveh and a Ba'al Mum are disqualified due to themselves, unlike a Chalal, who is disqualified due to others (his mother).

R. Tarfon agreed to R. Akiva.

Rishonim

Rashba (619): If Shimon slaughtered many animals, and checked the knife only twice afterwards, and then Levi came to slaughter and found the knife dented, Shimon is suspected. Whatever he slaughtered, and the Kelim used to cook them, are forbidden. A case occurred in which twice a Shochet was found to sell Nevelah, and they forbade his Kelim retroactively.

Pri Chodosh (YD 1:9): It seems that Shimon was suspected twice of not checking the knife. They did not depose him the first time, and he did not accept to be a Chaver (trustworthy) in between these two times. What he slaughtered was disqualified retroactively, i.e. from the first suspicion until now. Any salted meat from before the first suspicion is Kosher. This is because Shimon's Re'usa is only after the first suspicion. Likewise, at the end he discusses a case in which they forbade Kelim used for meat slaughtered after the first Nevelah, since he needed to accept Chaverus, but he did not. If today we found out that he sold a Nevelah 10 days ago, we forbid from then. The Rashba preferred to teach about a case that occurred. He does not forbid retroactively from the first Shechitah. If he did, he would not have supported this from a case in which they forbade after two Nevelos. Do not say that after two times he is like totally Mezid, therefore we forbid retroactively. Firstly, even if he is established to be a total Rasha, we would not forbid retroactively his entire life. Now he soured! Also, the Rashba requires three times to make a Chazakah that he was Mezid.

Poskim

Shulchan Aruch (YD 1:1): If they tested one who slaughters and checks, and it was found that he does not know (the Halachos), if he once received a Kabalah (certification), we do not forbid retroactively what he slaughtered, for we say that now he messed up. If he never received certification, everything he slaughtered is Terefah. Also, one must Kasher the Kelim in which was cooked meat that he slaughtered.

Shach (YD 1:8): Darchei Moshe asked why this is different than an animal that was found to be Terefah. The cheese made from its milk is Kosher if we can say that the animal became Terefah only now, because most animals are Kosher. We leave it in its Chazakah. He said that there is different, for most of all animals are Kosher, but most of all people are not expert about Shechitah. Only the majority who slaughter are expert. Therefore, this is not considered a Chazakah due to a majority. Also, we can say that the animal left life (i.e. became Terefah) only just before Shechitah. I distinguish, for there we can say that it was Kosher and now it became Terefah, but surely one was not expert from birth. We do not say that he learned and forgot. Also, it is not normal to forget laws of Shechitah, since one (who slaughters) must regularly learn them. If he received a Kabalah, we must say that he (learned and) forgot. Perhaps this is included in the Rema's words. Therefore, we cannot ask from a Mikveh (found to be deficient - 201:71). All Taharos that relied on it are Tamei retroactively. However, in any case it is not difficult, for here there is a Chazakah and a majority (most who slaughter are experts). There, there is no majority. Alternatively, here it is a Sefek-Sefeka (two doubts). There are other ways to distinguish. Based on my words, if one used to check, and an animal (that he declared Kosher) was found to be Terefah due to negligence, and not due to ignorance, letter of the law the Kelim are Kosher. We apply the Chazakah that until now he was Kosher. I said so in Siman 119 in the name of the Bach. Also the Maharshal says so.

Bedek ha'Bayis (YD Sof Siman 119): Orchos Chayim learns from the Tosefta (Bechoros 3:5) that one who is suspected of idolatry is suspected about all Mitzvos, but not retroactively. If Ploni slaughtered or removed Chelev, and later that day was Memir Daito (became an idolater), everything is Kosher

Pri Chodosh (1:9): Chulin 39b proves this. If one slaughtered and afterwards intended to throw the blood to idolatry, they did not permit or forbid. This is because there are grounds to say that he slaughtered for idolatry. However, if an hour passed and he slaughtered another with intent, surely this does not prove that also the first was for idolatry. The first is totally permitted. The Bach, Maharshal and Shach say so.

Bach (119:6): If one checked and slaughtered for others, and an animal (that he said is Kosher) was found to be Terefah, the first time, letter of the law we leave him on his Chazakah, and we do not forbid his Kelim. Even so, it is proper to be stringent due to Safek. Since now he is found to be suspected, perhaps he was already suspected. It is according to the judge's judgment. If there are Raglayim l'Davar (grounds to support) that he did so only now to avoid a big loss due to a Terefah, we can be lenient about Kelim. If there are no Raglayim l'Davar and it is a single Safek whether he did so several times and the Kelim because forbidden, we can be Machshir them.

Taz (119:16): Even though Maharshal is lenient about one (who sold a Nevelah once), it seems that we should forbid the Kelim retroactively in any case of Safek, even the first time.

Shev Shematsa (3:4): Bedek ha'Bayis (above) says that if Ploni was Memir Daito (became an idolater), he is not suspected retroactively. If he slaughtered or removed Chelev, and later that was Memir Daito, everything is Kosher. I found a Teshuvah of later Ge'onim (14) that is stringent about one who slaughtered. We leave the animal in its Chazakah (that it was not slaughtered), and (also) Ploni is now a Rasha. This is like a Mikveh that was measured (and found to be deficient. Anything Tamei immersed retains its Chezkas Tum'ah.) Also Tevu'os Shor (2:32) and the Bach are stringent about Shechitah. However, the Shach and Pri Chodosh hold that obviously, we do not forbid retroactively. Ploni's Chezkas Kashrus is intact until he was Memir. Why is he lenient? If a knife was checked, and after Shechitah the knife was found to be nicked, we hold like Rav Huna, who says that the Chazakah of the knife (it used to be good), which now has a Re'usa, does not uproot the animal from Chezkas Ever Min ha'Chai (Chulin 10a). He brought Tosfos, and said that all Tosfos' answers do not apply here. This is like a Mikveh found to be deficient. Just like there we can say that it steadily loses water, here we can say that he steadily was becoming more evil. Tevu'os Shor rejected the Pri Chodosh's proof from one who slaughtered and afterwards intended (Chulin 39b). He says that even though the Maharshal (Chulin 1:7) brought a Teshuvah to be lenient, it is not clear why and he did not explain the reason. We do not reject everything above regarding an Isur mid'Oraisa due to the Teshuvah.

Shev Shematsa: The rule is that we do not project the current status retroactively, except for cases like a Mikveh found to be deficient or a knife found to be nicked, or if one slaughtered and he was found to be totally ignorant (Taz 1:6). In all these cases we do not know when this happened. However, if a Shochet was Memir Da'as, we do not have a Safek that perhaps he did so also earlier, since there is no doubt about when this Aveirah (the one we know about) occurred.

Pischei Teshuvah (5): The Taz forbids retroactively. Avodas ha'Gershoni (15) proved that we do not forbid retroactively for one who is suspected. Mayim Rabim (YD 23) agrees, i.e. if one's Yetzer Ra forced him to transgress, but if he is suspected due to laziness, he is suspected retroactively. Bris Avraham (YD 7) permits retroactively; he said that this distinction requires investigation.

Pischei Teshuvah (6): Beis Yakov (4) says that retroactively, his Shechitah is Vadai Terefah, since Chezkas Isur of the animal joins with the Shochet's current Pesul.