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Answer: There are ample sources on the premise that certain Rabbinic violations of Shabbat are waived to protect holy articles, including tefillin. The mishna (Eruvin 95a) says that one who finds tefillin in an unprotected place may wear them in order to enable him to bring them to a secure area without carrying. The gemara (ibid. 97a) says that if it is not feasible to wear (all of) them, he may carry them in intervals of less than four amot. The gemara and poskim take for granted that muktzeh does not preclude such actions.
Bemare Habazak - Rabbis Questions (656)
Rabbi Daniel Mann
513 - Listening to the Megilla with Limited Concentration
514 - Batim of Tefillin on the Floor on Shabbat
515 - Raffle on Shabbat
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However, these sources are insufficient to have permitted you to pick up the batim because you asked about empty batim, not tefillin. It is true that they were once part of tefillin¸ but when something breaks off from a kli, it becomes muktzeh (Shulchan Aruch, OC 308:6). Even if the batim are not broken but can be used again in the future for tefillin, they are not considered a kli now since their return to tefillin requires an expert (see Chayei Adam 73:13) and also it is forbidden to do so on Shabbat.
Therefore, we must return to the idea that saving tefillin from disgrace allows violating certain Rabbinic prohibitions. It is difficult to suffice with the aforementioned mishna, as commentators understand that there is concern there for great disgrace (see Rashi, Eiruvin 75a; Dirshu 301:109). Maybe, then, here it is sufficient to cover up the tefillin (see Shulchan Aruch, OC 301:42). However, we do find leniency regarding holy things that are on the floor. The contemporary sefer Shalmei Yehuda (1:4) cites Rav Elyashiv and Rav Binyamin Zilber as allowing one to pick off the floor even non-useful scraps of paper with Torah writings on them, which are muktzeh, to save them from disgrace. Batim that were already used for tefillin have the kedusha at least of tashmishei kedusha, as they housed the sacred tefillin scrolls, and they require geniza (Ginzei Hakodesh 6:6). (The bayit of the tefillin shel rosh is even more sacred due to the letters shin on their sides.) Therefore, if it is permitted to pick up the geniza-destined piece of paper when it is muktzeh, it should likewise be permitted and proper to lift up the batim. This is not a trivial conclusion. One could distinguish between the paper that is directly on the floor and the batim that are in the bag. Additionally, some Acharonim forbid (see Orchot Chaim 19:(56)) picking up sacred muktzeh articles without special grounds for obviating the problem of muktzeh.
When considering everything, though, we agree with your intuition to pick them up. In this case, one who wants to be stringent on muktzeh is being lenient on disgracing something with sanctity. We will not suggest complicated means of being machmir for both with creativity because, generally, this is not something that the poskim prescribe in such cases.

Chemdat Yamim Moreshet Shaul: Twin Foundations
Based on Siach Shaul, Pirkei Machshava V’Hadracha p. 690
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P'ninat Mishpat P'ninat Mishpat: Realtor’s Fee on Large Commercial Building – part I
(based on ruling 85031 of the Eretz Hemdah-Gazit Rabbinical Courts)
(based on ruling 85031 of the Eretz Hemdah-Gazit Rabbinical Courts)

Chemdat Yamim Moreshet Shaul: The Goal of an Agricultural Yeshiva – part I
Based on Siach Shaul, Pirkei Machshava V’Hadracha p. 263 (address at the laying of the cornerstone of the Yeshiva Chakla’it in Kfar Haroeh)
Based on Siach Shaul, Pirkei Machshava V’Hadracha p. 263 (address at the laying of the cornerstone of the Yeshiva Chakla’it in Kfar Haroeh)

Re'e NEVER EXTREME EXCEPT ISRAEL
Parshat Re'eh
Judaism is against extremism, so how can we understand the seemingly extreme statements found in our sages in favor of living in the Land of Israel and against living in Chutz laAretz? The article deals with the seeming contradiction between the strength of Free-Will and the strength of being influenced by our surroundings.

Ekev DANCE FOR ISRAEL- FOR YOUR BENEFIT
Parshat Eikev
Description: The 7 Haftarot we read after Tisha B'Av ("Shiva D'Nichemta") surely get us excited that they're coming TRUE, and awaken us to yearn, dance & join the return to Zion! The short article also deals with the problems and solutions facing the American Jewish community as discussed at a recent panel, as well as the question why Jews come from America to Israel to help when we face problems, but Israelis don't come to aid Jews in America when they face anti-Semitism.

P'ninat Mishpat P'ninat Mishpat: Complaints about Contractor’s Work – part II
(based on ruling 83037.1 of the Eretz Hemdah-Gazit Rabbinical Courts)
(based on ruling 83037.1 of the Eretz Hemdah-Gazit Rabbinical Courts)

Chemdat Yamim Moreshet Shaul: Twin Foundations
Based on Siach Shaul, Pirkei Machshava V’Hadracha p. 690
Based on Siach Shaul, Pirkei Machshava V’Hadracha p. 690

D'varim Judaism’s Social Vision
Re’eh
Giving is more than an act of generosity—it is an essential part of human dignity that belongs to everyone, rich and poor alike. The ultimate goal of help is to empower others to stand on their own.

Kuzari -Rabbi Ari Shvat Kuzari class 9 - "Seeing is Believing" (parag. 21-30)
These paragraphs elaborate on the theme that seeing and knowing is better than any attempt to prove logically, and begins explaining the difference between Israel and gentiles.








