Question
Can the potential energy in a simple harmonic motion be negative? Will it be so if we choose zero potential energy at some point other than the mean position?

Answer

No. It cannot be negative because the minimum potential energy of a particle executing simple harmonic motion at mean position is zero. The potential energy increases in positive direction at the extreme position.
However, if we choose zero potential energy at some other point, say extreme position, the potential energy can be negative at the mean position.

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