The Mishnah (3:3) teaches that until the point that the megillat sotah is wiped out in the water for mei sotah, the sotah can decide not to continue. This is the case even without admitting to the affair. Even though she can stop the process, they would need to be divorced and she would lose her ketubah. The Mishnah then explains what to do with the items that were prepared for the process.
The Mishnah explains that the korban mincha that she brought would not be offered. Instead, it is burnt on the deshen along with other korbanot that became invalid. The megillat sotah cannot be use for another sotah so it is "nignezet". Rashi (20a) explains that it stored in the side of the heichal -- in geniza -- much like other kitva kodesh that can no longer be used. The Tosfot (20a) however cite the Yerushalmi that explains that the megillah was placed under the door hinge of the heichal so it could be ground.
The Shayarei HaKorban asks that we learn in Makkot (22a) that it forbidden for wipe out the name of Hashem (which was written on the megillat sotah). This is based on two pasukim following one after the other: "... you shall wipe out their names (of avodah zarah). Do not do so to Hashem..." (Devarim 12:3-4). That being the case, how does the Yerushalmi understand that it was put in a place in order for it to be ground. It would be prohibited for anyone to open or close that door.
The Shayarei HaKorban suggests that the Yerushalmi does not agree with that exposition of the Gemara. He uses this understanding to answer a question posed by the Kesef Mishnah. The Kesef Mishnah ask why the Rambam omitted this detail of where the megillah was placed when it is mentioned in both the Yerushalmi and Tosefta. The Shayarei HaKorban answers that since the Rambam rules like the Gemara in Makkot, he cannot rule like the Yerushalmi which contradicts it.
The Ridbaz however explains that the Yerushalmi earlier (2:4) maintains that the megillat sotah does not makes hands tameh. Recall that the Chachimim made a gezeira such that kitvei kodesh makes hands tameh. The Yerushalmi maintains that the megillat sotah is not defined as kitvei kodesh because from the outset it was written to be wipe out in the mei sotah. Consequently, there is not issue with it being ground.
The Ein Yitzchak (OC 5:27 however explains that while the answer is sufficient to allow wiping the general text, it does not justify the destruction of the name of Hashem. Furthermore, he finds the answer of the Shayarei Korban difficult considering that the Yerushalmi earlier in Sotah implies that the prohibition of wiping the name of Hashem also applies to the megillat sotah. The Ein Yitzchak therefore explains that the biblical prohibition is only when the name was written be'kedusha. He explains that when the kohen wrote the megillah we would have stipulated that the name would only get kedusha if the process continued till it was wiped in the mei sotah. Since the process was stopped, it did not have kedusha, so the prohibition does not apply.
The Chazon Ish (Yadayim 8:17) explains that the prohibition of wiping out Hashem name applies even in a case where it should not have been written. In this case, since the sotah process was stopped, it is now clear that it should have not been written. He however explains that the megillah would have been folded and taken time for it to wear. Consequently, the grinding would be defined as indirect -- gerama. In this case where it should not have been written, it is permitted through gerama.
The Yalkut Biurim however cite the Tifferet Tzion who has a different understanding of the follow of the Yerushalmi. The question above has been based on the following reading. "The megillah was placed under the tziro (hinge) of the heichal. Why? For it be ground. The was a small window there in which the water was poured away..." He however suggests that the Yerushalmi should be read as follows. "The megillah was placed under the tziro of the heichal. Why?! For it get ground?! [That would be prohibited! Rather] there was a small window there [in which it was placed]. The water was poured away..." With that reading, the Yerushalmi rejects the idea that the megillah was destroyed and the original question no longer applies.^1^
^1^ Nevertheless, the question would still apply regarding the Tosfeta that clearly explains that the megillah was ground under the hinge.
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