Remember this rule: among the trickiest halachot to decide are those where there is a conflict between competing halachic preferences. While halacha requires us to act in manner a and in manner b, how do we know how to act in cases where a and b are mutually exclusive? One must either find sources that deal with a case where the two issues conflict or to independently decide (intuitively or otherwise) which issue should have precedence.
There is a rule that, out of respect for the congregation, one should not roll the sefer Torah to the right place while the congregation waits. For this reason, the gemara[1] relates, the Kohen Gadol would read part of the Torah reading on Yom Kippur by heart rather than rolling the sefer from Acharei Mot to Pinchas. Nowadays, we do roll the sefer Torah when there is a need, under the assumption that the congregation is willing to compromise its honor under the circumstances.[2] Another rule found in that gemara is that one should not do anything that might imply that a sefer Torah is pasul when indeed it is not. For that reason, they did not have a second sefer on hand for the Kohen Gadol to switch to.[3]
While we have found no discussions among the Rishonim on a case where we have to choose between rolling a sefer Torah and casting aspersions on it, Acharonim do discuss it. The common case is where the person who has peticha[4] gives the chazan the wrong sefer. In the siddur of Rav Yaakov Emden, two opinions are mentioned: to return the sefer and take out the right one; to roll the one that was taken out. Rav Moshe Feinstein[5] says that it is hard to determine which factor takes precedence, but if the congregation is willing to forgo its honor, the sefer Torah should be kept out and rolled. He continues that if someone (not necessarily the rabbi) already gave instructions to return the sefer Torah to the aron, then there is a concern that overruling him will cause dispute or embarrassment. This is treated like a situation where the congregation does not withdraw its right to honor, and we return the sefer.
Our situation is different in two ways. First of all, if one does not switch sifrei Torah, it is necessary to roll both of them, which takes longer and increases the chance of disruptive discussion among congregants. More fundamentally, there should be no disgrace to or aspersions on the sefer Torah we would “pass up” by switching. After all, it would soon get its turn to be used as the second sefer. This is probably the rationale of the Sha’arei Ephrayim[6] (a 19th century work on the laws of kri’at haTorah) that says that if one opens the sefer for maftir instead of that for Bereishit on Simchat Torah, he should close it and switch sefarim rather than roll it. The Bi’ur Halacha[7] concurs with this analysis.
Another halachic factor which is all but ignored in the Acharonim’s treatment of this question is the concept, “ein ma’avirin al hamitzvot” (we don’t pass over mitzvot or, in this case, the sefer Torah to be used for a mitzva). One reason that it might not apply is that one person’s error in taking the wrong sefer should not bind the whole congregation to suffer.[8] Whatever the reason, though, the consensus is that, in the case of switching two sifrei Torah that will both be used, we opt to switch the sefarim rather than roll.