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I've found the problem. I had been using the clone() function to create a copy of the mesh and then compute the bounding box with the applyMatrix4 on this copy, but it turned out that the clone() function does not copy also geometry and material. So I've created a new mesh instead of a clone and then I've passed to it a clone of the existing geometry and material. Now, compute the bounding box on a real copy of the geometry does not affect the original one and the onClick on the original mesh keeps working.

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Answer selected by Draco112358
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