Nah, as others have pointed out, what you do is run the Shor's algorithm, then verify it. If it's wrong, run Shor's again. If it's right, you know you have the factorization. In this way, you can be 100% sure that you've correctly solved the problem, even if Shor's only provides the correct answer some percentage of the time.
What I don't fully understand is why 48% makes this impractical. Having not read TFA, the only way I can imagine that would be the case is if somehow not having exactly a 50% chance
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