Discovered after the reading was finished:[1]

If the invalidating mistake was discovered in the Sefer Torah only after the reading was complete, nevertheless, the congregation is Yotzei and a new Sefer Torah does not need to be removed to have the reading repeated. [Furthermore, even if the mistake was already known before the reading, and it was accidentally used, one is Yotzei.[2] However, if this occurred by Parshas Zachar or Parah, and it was discovered that Shabbos, then it is to be repeated in a Kosher Sefer Torah.[3]]

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[1] Poskim in next footnote; M”B 143:13; Piskeiy Teshuvos 143:10 

[2] Ledavid Emes 1:8; Kneses Hagedola 282:9; Yabia Omer 8:15-12

[3] Piskeiy Teshuvos ibid