Gemara

(Beraisa): If a woman miscarried the form of an animal, and a fetal sac, if they are not tied together, perhaps the sac of the animal dissolved, and a fetus in the remaining sac dissolved. We are stringent for both possibilities.

37a - Question: Do clean days during Tum'as Yoledes count (towards the seven clean days that a Zavah must count?)

Answer #1 (Abaye): They are not Soser, but they do not count.

Answer #2 (Rava): They are not Soser, and they count.

54a - Support (for Rava - Rav Kahana - Beraisa): If a woman saw blood for two days (of Zivah), and miscarried on the third day, and she is unsure what she miscarried, she is Safek Zavah, Safek Yoledes. She brings a Korban, but it is not eaten;

Clean days of Leidah count towards the seven clean days.

Objection (Rav Papa): Perhaps she may count only the second week of Safek Tum'as Yoledes, for perhaps Tum'as Yoledes does not apply then, i.e. if she did not give birth to a female!

Answer (Rav Huna brei d'Rav Yehoshua): (If Yemei Leidah would not count,) we must be concerned lest she gave birth to a female!

Rav Kahana's answer stands.

Shevu'os 19a (Beraisa): If there are two paths, and there is a Mes under one of them, so anyone who walks on the path becomes Tamei, if a man walked on one path, and later on the other path, and then entered the Mikdash, he is liable.

Pesachim 10a (Mishnah - R. Yehudah): If Reuven walked on one path, and Shimon walked on the other, and they touched Taharos:

If they ask separately, we tell each of them that his Taharos are Tehorim;

If they ask together, we are Metamei the Taharos of both of them.

R. Yosi says, in either case both Taharos are Temei'im.

(Rava): If they ask at the same time, all agree that we are Metamei both. If they ask at different times, all agree that we are Metaher both;

They argue about one who asks for himself and his friend. Is this like asking at different times, or is it like asking at the same time?

Bechoros 42b (Beraisa): The widow of a Tumtum (his (or her) genitals are covered, so we cannot tell his geneder) can do Chalitzah, but not Yibum.

The Tana holds like R. Yosi b'Rebbi Yehudah;

(Beraisa - R. Yosi b'Rebbi Yehudah): A Tumtum does not do Chalitzah, lest he (i.e. the skin coveringhis genitals) be torn and found to be a Seris Chamah (one who does not develop like a normal male).

He does not do Chalitzah, lest he be torn and found to be female;

Even if he is male, perhaps he is a Seris.

Rishonim

Tosfos (27a DH Chomer): If a woman miscarried the form of an animal and a Shilya, according to Chachamim (who say that Tum'as Yoledes applies only to human forms) we are concerned lest there was a child in the Shilya. She adopts the stringencies of Yoledes Zachar and Yoledes Nekevah. A Sefek-Sefeka should exempt from the stringencies of a female! Perhaps there was no child, and even if there was, perhaps it was a male! We do not say so, for perhaps she will see blood on day 41, and a Sefek-Sefeka would similarly permit it. Perhaps she did not give birth at all, and on day 41 she is Shomeres Yom k'Neged Yom (e.g. if she became Nidah between 8 and 18 days ago). And even if she gave birth, perhaps the baby was a female, and it is Dam Tohar. We cannot be lenient about both of these, for they are contradictory. Therefore, we are stringent about both of them. We must say so to explain the Mishnah of one who does not know whether or not she miscarried. A Sefek-Sefeka would exempt from Tum'as Yoledes Nekevah if not that a contradictory Sefek-Sefeka (could exempt from Nidah on day 41).

Tosfos (37a DH Abaye): Rav Papa says that the second clean week counts like seven clean days, for perhaps she gave birth to a male. We can say that Rav Huna disagrees, even though there is a Sefek-Sefeka. We must be concerned for a female, since at the end of Yemei Tohar there is a Sefek-Sefeka that contradicts this one, like I explained above.

Ohr Same'ach (Hilchos Shechitah 8:12): I say that we cannot rely on the Sefek-Sefeka because if she will fix a Veses (of seeing the same day every month, or after a certain interval) during the seven days after the miscarriage, an opposing Sefek-Sefeka would say that she did not fix a Veses. Perhaps she gave birth, and she cannot fix a Veses through Dam Leidah. And even if she did not give birth, perhaps she saw blood and became a Zavah, and one cannot fix a Veses during the days of Zivah.

Poskim

Maharit (2 YD 2) Question #1: A Tumtum's wife does Chalitzah, but not Yibum. We establish this like R. Yosi b'Rebbi Yehudah, who says that perhaps he will be torn and found to be a Seris, therefore he may not do Yibum. A Sefek-Sefeka should permit Yibum. Perhaps the Tumtum is really a female, and even if he is a male, perhaps he is not a Seris! Similarly, his wife should not need Chalitzah. Perhaps the Tumtum is really a female, and even if he is a male, perhaps he is a Seris!

Suggestion: We are not concerned lest he is a Seris, for we follow the majority. If Ploni was Mekadesh a girl of three years old, other men are killed for Bi'ah with her. We are not concerned lest she is an Ailonis (one who does not develop like a normal female), and Ploni did not intend to be Mekadesh an Ailonis! This is because we follow the majority.

Rejection: A Tumtum is different (than regular men), so we are concerned lest he is a Seris. We find that R. Yehudah considers him to be a Vadai Seris.

Question #2: We are concerned for Tum'as Yoledes Zachar and Yoledes Nekevah when one miscarried a Shilya with an animal form, even though perhaps the Shilya is due to the animal, and even if it was a human baby, perhaps it was a male.

Answer (Maharit): Tosfos answered Question #2. We do not permit due to Sefek-Sefeka when we would permit also something else due to a contradictory Sefek-Sefeka. Do not say that we can permit just due to the Safek that she is regular Nidah, for we would not permit due to a single Safek. This answers also Question #1. If we would permit Yibum, we would also permit marrying a stranger without Chalitzah.

Suggestion: The Tumtum is different, for the Safek is not in one person. Even if he has two wives, and one does Yibum and one marries a stranger, each has a Sefek-Sefeka to support her. All th Sefekos regarding Nidah affect one woman, therefore she may not be lenient in both directions.

Rejection (Maharit): If different people walked on two paths and made Taharos and asked one after the other, we are Metaher both of them, even though in any case one of them is Tamei. However, we do not distinguish. Even if the woman wants to be lenient now, and says 'if I will see on days 34 and 41, I will be stringent', Chachamim forbid and decreed to be stringent even now.

Suggestion: There we are stringent because both Sefekos could affect one person. Regarding the Tumtum, they cannot!

Rejection (Maharit): Also regarding the Tumtum, perhaps one widow will remarry, become widowed again or divorced, and then marry the Yavam.

Sifsei Da'as (YD 110 veha'Mechudashim, Sof 1): The Maharit says that Chachamim decreed that she not remarry without Chalitzah, lest she be widowed and married the Yavam, and contradict herself. If one Safek alone contradicts, it is forbidden. The Torah forbids to remarry without Chalitzah and then to do Yibum, for this relies on only one Safek, that the Tumtum is a female. If he is a male, she Vadai sinned. If so, this is a single Safek, and the Torah forbids it. The Rambam holds that the Torah permits all Sefekos. If so, the Isur is only mid'Rabanan. If so, why is she forbidden to just remarry? This is like a decree against a decree. This requires investigation.

Aruch ha'Shulchan (110:117): There is no proof from a Tumtum. Even if we would say that we permit every Sefek-Sefeka without clarifying it, even though one could clarify, this refers to something that is not normally clarified. It is normal to clarify a Tumtum's status through tearing (the skin covering the genitals). Therefore, surely one must do so. We cannot rely on the Safek that the Tumtum is a female. Even if we would say that one need not clarify, surely one may not rely on such a Safek, lest the Tumtum be torn and it will be revealed that we erred.

Pri Chodosh (YD 110 Klalei Sefek-Sefeka): The Rambam holds that the Torah permits all Sefekos. If so, why did the Gemara ask why Chachamim forbade a Shtuki (one who is unsure who his father is)? They forbade him like all Sefekos! The Maharit answers that the Torah permitted a Safek Mamzer like Vadai, not just due to Safek. Therefore, he may marry a Mamzeres and a Bas Yisrael, even though these contradict the other. (Whether he is Kosher or a Mamzer, he is forbidden to one of them.) Seemingly, we could say that the Torah distinguishes marrying both at once, or one after the other. However, this is wrong. If they are forbidden at once, they are forbidden one after the other. If one of two paths is Tamei, if Reuven and Shimon each walked on a different path and made Taharos, if they asked one after the other, all agree that they are Tehorim. If they asked at once, both are Teme'im. Tosfos (10a DH b'Vas) says that this is only mid'Rabanan. This is reasonable. The Torah does not distinguish. However, it is not clear whether the Torah permits a Safek Mamzer even when it is Tartei d'Sasrei. We cannot learn from the case of two paths, for that Safek depends on two different people. Since Safek Tum'ah in Reshus ha'Rabim is Tahor, this is even if they ask at the same time. Each can say 'the other went on the Tamei path.' Regarding one person, we cannot permit Tartei d'Sasrei.

Pri Chodosh: There is a proof from Shevu'os 19a. If one went on one path, and later on the other path, and then entered the Mikdash, he is liable. Tosfos explains that it discusses any Safek Tum'ah in Reshus ha'Rabim. Even though the Torah permitted every such Safek, this does not apply to Tartei d'Sasrei. Tosfos (Kesuvos 27a DH v'Im) says similarly that when different people went on the paths and made Taharos and asked separately, we rule that both are Tehorim, but one person may not eat both, for then he Vadai eats Tum'ah, like it says in Shevu'os. When the Torah forbids due to Tartei d'Sasrei, one is even lashed for it.

Pri Chodosh (7,8): When there is Tartei d'Sasrei, the Torah forbids a Sefek-Sefeka regarding two different people, but forbids regarding one. There is no difference whether the Sefekos occur at the same time or one after the other, whether it is to be lenient or stringent.

Note: I am unsure what he means 'to be lenient or stringent.' We are stringent about Tartei d'Sasrei! Perhaps he means that one may not be stringent in a way that leads to a leniency.

Pri Chodosh (3): Tosfos holds that when there are contradictory leniencies in Sefek-Sefekos, we are stringent about both of them. However, since we are lenient about a Safek mid'Rabanan, we can be lenient even if there is Tartei d'Sasrei regarding two people. This is when the matter is not evident, e.g. a Safek whether it was day or night. If a matter comes in front of us, we are not lenient about both of them, for this would make Divrei Chachamim look ludicrous.