Sotah 41a - Mistake in Sefer Torah

The Rama (o.c. 143:4) paskens that when a mistake is found in a sefer torah, if the reader is at a place where he can stop (3 pesukim into the parsha and no less than 3 until the end of the parsha) then the o'leh should make a bracha achrona on the first sefer, and then take out a second sefer with a new o'leh. However, if the mistake is in a place where stopping is not an option, then a second sefer should be taken out and read from the place where the reader is up to without making a bracha rishona on it at all.

This position of the Rama is actually a complicated compromise of various Rishonim. The Bach however rules like the Mordechai that under all circumstances a bracha achrona should be made on the pasul torah.

The Mordechai's souce is from the gemara today where Reish Lakish says that there isn't an option to take out a second sefer torah because a new sefer torah would require a new bracha. The gemara implies that a new sefer requires a new bracha rishona. Based on this the Mordechai claims that one cannot take out a new sefer torah and continue reading without a bracha, because a new sefer torah would require a new bracha. Therefore the mordechai concludes that the bracha achrona should be made on the pasul torah. Both the Shach and Taz try to justify the position of the Rama that allows one to take out a second sefer and continue reading without a bracha (if the mistake was found in a place that you can't break).

The Shach (y.d. 279:2) says that in the case of the gemara when the original bracha was made on parshas achrei mos, he didn't have in mind for the bracha to go on the reading of "ach b'asar" and therefore would require a new bracha, but in our gemara where his intent originally was on this parsha that is being read, since he had intent to make a bracha on this section he can read this section even on a second Torah without requiring a new bracha.

The Taz tries to understand why the gemara assumes that a new sefer torah would require a new bracha, since he originally would have had in mind when he made the first bracha that they would bring a new sefer for the second reading. It should be like one who has in mind to eat apples and oranges and makes a ha'etz on the apples, he doesn't need a new bracha on the oranges even though they are only brought out later. It must be that the requirement of a new bracha is because it is a separate chiyuv of Torah reading which requires a new bracha. This applies only when the second reading is a new obligation but when it is only a make up for the first reading (because the torah was passul), it is not necessary to make a new bracha.