Twilight knowing where the time spell was isn't actually a paradox, because she DIDN'T know. She checked the whole library for a time stopping spell and only the Starswirl wing was left. And even then, Pinkie ended up finding the time travel spell (not what they were even looking for) at random, which is the only reason Twilight knew where it was.
The time paradox is why she was so worried that she traveled back the first time, but stable time loops are always like that.
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"That is why war is so tragic. To win means to make victims of your opponents and give birth to hatred." - Kratos Aurion, Tales of Symphonia