http://revach.net/article.php?id=4756

Section: Hanhagos   Category: Minhagim
Taking A Break Before Tekias Shofar
The Minhag Yisroel Torah says that the Minhag of taking a break before Tekias Shofar is accepted and practiced across the entire spectrum.  Why do we take a break?

He brings from the Nefesh Chaya who says that it is assur to daven more than three hours straight.  He brings proof to this from the Vilna Gaon in Mishlei as well as the Ramban in Mishpatim where Moshe lifted his arms to fight Amaleik.  Therefore every shul has at least a short break where people go out and then come back in, or some other clear sign that davening is over and a new davening will begin.   

The issue is that the Minhag is to leave the Sefer Torah on the Bimah during the break, since we only put it back after Tekias Shofar, and it is assur to leave Shul while the Sefer Torah is out.  The Pri Megadim says that it is permitted to leave it out as long as a Minyan stays in Shul but the Elef HaMogen says even if a minyan remains it is still assur.  However people leave even if there is no minyan remaining.

Therefore the Ktzei HaMateh says that the Sefer Torah should be put back in the Aron during the break. Others say that covering the Torah with a Talis is like putting it back in the Aron.  However the Shu"t Bais Yisroel argues and says that even if there is no minyan it is okay.  The issur, he says, is only if davening is over and the people leave to go home and not come back.  Since here they are planning to return shortly to resume davening there is no problem of leaving the Torah outside the Aron.