Gemara

(Shmuel): If the witnesses' hands were cut off, the defendant is not stoned, since we cannot fulfill "Yad ha'Edim Tihyeh Bo va'Rishonah."

Question: If so, witnesses without hands should be invalid from the beginning!

Answer: "Yad ha'Edim" teaches that if they had hands from the beginning, those hands must kill him.

Support (Beraisa - R. Yishmael): If a city does not have a street, it cannot become an Ir ha'Nidachas (because the verse says that we gather everything into the street);

R. Akiva says, if it has no street, we build a street.

They only argue whether or not the street must be there from the beginning, but all require a street!

Tana'im argue about Shmuel's law:

(Mishnah): If a Metzora does not have a right thumb, big toe or ear, he can never become Tahor (blood of the Asham must be put there);

R. Eliezer says, it suffices to put it in the place of the missing limb.

R. Shimon says, it suffices to put it on the left thumb, toe or ear.

Menachos 5a (Rav Papa): Regarding Taharas Metzora it says "Zos Tihyeh Toras ha'Metzora". This teaches that everything must be in order.

19a (Mishnah): The four species used for Taharas Metzora (cedar, hyssop, scarlet thread and birds) are Me'akev each other. It says "Zos Tihyeh Toras ha'Metzora". This is (Me'akev) as if it said 'Chukah'.

Nazir 46a (Rav): A Nazir must wave (the Zero'a and Lechem to become permitted to become Tamei and drink wine). This is unlike Chachamim. They permit even without shaving, all the more so without waving! Rather, it is like R. Eliezer (who permits after all the actions).

Beraisa: "Zos Toras ha'Nazir" - whether or not he has hands.

Just like a handless Nazir need not wave, also one with hands.

Rishonim

Rambam (Hilchos Sanhedrin 14:8): If someone sentenced to death resisted execution and Beis Din could not restrain him to administer the proper Misah, the witnesses may kill him in any way possible. Others may not kill him first. Therefore, if the witnesses' hands were cut off, he is exempt. If the witnesses had no hands from the beginning, others may kill him. This refers to Misos other than a murderer. If a murderer was sentenced, we pursue him in any way and through any person, until we kill him.

Me'iri (45b DH Af): We kill a murderer in any way and through any person. For other Misos, we put him in Kipah (a cell), and feed him barley and water, which causes his death.

Question (Magihah): Sanhedrin 81b connotes that Kipah is only for a murderer. The Rambam and Me'iri himself rule like this!

Bartenura (Nega'im 14:9): The first Tana says that a Metzora missing his right ear (or thumb or toe) can never become Tahor. This is only if he lost it after he became Tamei.

Question #1 (Tosfos Yom Tov DH v'Ein): If he was missing it before becoming Tamei, it is not Me'akev. Even Shmuel requires the verse ("Yad ha'Edim Tihyeh Bo va'Rishonah") as it is written only if the witnesses had hands at the time they testified. The Rambam rules like Shmuel regarding stoning, but regarding Metzora he does not distinguish when the Metzora lost his ear! Regarding Nazir he says that the verse is only l'Chatchilah!

Answer #1 (Boaz 5): "Yad ha'Edim" connotes the hand the witnesses had at the time of (seeing or giving) testimony. Regarding Metzora it does not say 'Yad ha'Metzora', therefore it does not matter when he lost his hand. A Nazir is permitted through Zerikas Dam of his Korbanos. His Heter does not depend on shaving and waving.

Question #2 (Tosfos Sanhedrin 45b DH Ein): The Gemara here says that Shmuel holds like the Tana who says that there is no Taharah for a Metzora without an ear. Perhaps the Tana normally does not require fulfilling the verse literally, only regarding Metzora, because it says "Tihyeh"! In Menachos (5a and 19a), "Tihyeh" teaches that everything about Metzora is Me'akev!

Answer (and Answer #2 to Question #1 - Tosfos Yom Tov ibid.): The Rambam holds that the Sugya in Sanhedrin argues with those in Menachos. He rules like those in Menachos, that "Tihyeh" teaches that everything about Metzora is Me'akev. He has a different source to rule like Shmuel, i.e. the Beraisa of Ir ha'Nidachas.

Question: If Edim w ere Huzmu after the Nidon was killed, we do not kill them (Makos 5b). If the witnesses themselves must kill the Nidon, they should be liable for murder!

Answer #1 (based on Si'ach Yitzchak Makos 5b DH Gemara): They cannot be killed because they were not warned. However, we should put them in Kipah, like a murderer who was not warned! (Also, R. Yosi b'Rebbi Yehudah holds that a Chaver (Chacham) need not be warned. We never heard that he holds that a Chacham witness is killed after the Nidon was killed! - PF) The Torah believes the latter witnesses over the former only before the Nidon was killed. If he was already killed, it is a Safek who is lying.

Answer #2 (Margoliyos ha'Yam 45a:12): The Torah totally believes the latter witnesses before the Nidon was killed, for then both of them merely said words, but not after he was killed, for then the first witnesses also did an action (killed him).

Note: According to this, if others killed the Nidon (e.g. a murderer), we should accept Hazamah afterwards to kill the witnesses!

Answer #3 (Si'ach Yitzchak 5b DH Tana): They also transgressed false testimony, so Ein Onshim Min ha'Din (we cannot punish like one who transgressed only murder, for perhaps this does not suffice to atone for them!)

Answer #4 (Einayim l'Mishpat Makos 5b:3 DH uv'Meforshim): Even though they lied, they are not called murderersm for they kill according to Beis Din. The Riva (Tosfos Shabbos 4a DH Kodem) says that one who allows his dough to finish baking on Shabbos because Chachamim forbade him (to peel it off the wall of the oven), he is exempt from Misah. The Rashba (Rosh Hashanah 16a DH Lamah) says that Bal Tosif does not apply to enactments of Chachamim.

Kli Chemdah (Shoftim 159a DH Emnam): The witnesses must begin the execution only when the Nidon does not confess. If he admits, since there are also witnesses, his admission helps, and he may be killed due to his admission, not through the witnesses. (Similarly, if Nisrafim and Niskalim became mixed, their admission helps to give the lighter Misah.) However, this is difficult, for no Posek says so. Rav Hai Gaon explains 'witnesses are not killed until they Mezim themselves', i.e. they admit to the Mezimim's words. If so, we should believe them and kill them even if the Nidon was killed! The Shitah Mekubetzes (Kesuvos 45a DH Hi) says that Rashi and the Rambam hold that if the witnesses of a Motzi Shem Ra were Huzmu, we cannot lash him due to a Safek. He says that she was Mezanah, and he will find other witnesses! He is lashed only if he admits. Perhaps Misah is different. The Rambam (Hilchos Sanhedrin 18:6) says that one may not be killed through his admission, lest one who wants to die falsely admit

Rashi (45b DH Yad): The verse discusses witnesses who had hands, and they were cut off. If they did not have hands from the beginning, this (whatever is closest to their hands) is their hands.

Ramah (45b DH Omar): The Gemara knew that witnesses without hands are Kosher for capital cases, for this is not listed among differences between monetary and capital cases.

Sefer ha'Kanah (in Margoliyos ha'Yam 45b:8): The Mishnah did not list among the differences a witness whose hand was cut off after he testified, for clearly this does not apply to monetary cases, in which there is no need for his hands.

Aruch l'Ner (45b DH Omar): If after the witnesses were Huzmu (perhaps this should say 'after they testified' - PF), their hands were cut off, what is the law? Do we say that since now they could not kill the Nidon, they are not killed? Or, since they could have killed him at the time of the verdict, we apply Ka'asher Zomam? We may learn from the Rambam (Hilchos Edus 22:1), without says that if one was found to be a relative or Pasul after the verdict, they are not punished like Zomemim (and the same applies here).