If a Sefer Torah is discovered to be invalid for use, a second Torah must be taken from the ark and used in its place. The question arises as to whether or not the disqualified scroll may be returned to the ark and stored there until the problem is corrected. After all, the ark is endowed with a Halachic status of Kedusha (sanctity), and the presence of an invalid Sefer Torah might perhaps constitute an infringement upon this special status.
This question was discussed by Rav Yechezkel Ben Yehudah Halevi Landau (1713- 1793, Poland), in his work "Noda Biyehuda" (Mahadura Kama, O.C. 9). The question hinges on the possibility of comparing this case to that of the "Shivrei Luchot," the remnants of the tablets that Moshe had broken upon his descent from Mount Sinai. According to one view recorded in the Gemara in Masechet Shekalim, the Shivrei Luchot were kept in the same ark used for storing the second tablets in the Mishkan (Tabernacle). At first glance, a disqualified Sefer Torah has a status similar to that of the Shivrei Luchot. Hence, the fact that the Shivrei Luchot were stored in the Aron (ark) in the Mishkan would prove that a disqualified Torah scroll may be returned and stored in the ark in the synagogue.
However, the " Noda Biyehuda" raises a number of possible refutations to this proof. For one thing, the original tablets were fashioned by the Almighty Himself, and were thus endowed with a special status of sanctity that remained even after Moshe shattered them. The same cannot be said, of course, about a Sefer Torah. Furthermore, it is possible that the ark in the Mishkan was initially constructed with the clear intent that it would provide storage for the Shivrei Luchot, and only for this reason was it permissible to keep the broken tablets there. We would then be unable to reach any conclusions regarding a contemporary ark on the basis of the ark in the Mishkan.
Although the " Noda Biyehuda" is inclined to forbid storing a disqualified Sefer Torah in an ark, an earlier source, the Sefer Ha'chasidim (by Rabbi Yehuda Ha'chasid, Germany, 1150-1217), writes explicitly (in Siman 534) that this is permissible, on the basis of the storage of the Shivrei Luchot in the ark in the Mishkan. Halacha indeed follows this view, that a congregation may keep a disqualified Sefer Torah in the ark, and in fact this is the widespread practice. However, the congregation must ensure to make a clear indication on the scroll that it is invalid for use, so that they do not mistakenly use it for the Torah reading, and they must correct the problem as quickly as possible, so as to minimize the risk of error.
Summary: If a congregation discovers that a Sefer Torah is disqualified for use, they may store it in the ark, provided that they make a clear, visible indication that it is not usable and correct the problem without any unnecessary delay.
