Hello, I am working on a local project so I cant put a playground, but the bug is when I make an instance of mesh it will take all of its properties correct and the scaling have a correct value but the value is negative like the mesh value is 90 the instance mesh value is -90 is there is a way to fix that, and when I try to change the scaling value to 90 manually the instanced mesh disappear.
Unfortunately it is almost impossible to help without a repro 
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Shot in the dark: if your meshes are coming from a gltf/glb file, try to set scene.useRightHandedSystem = true just after the scene creation and see if it helps.
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the whole model flipped 
the thing is that I did like a sample test on the playground of what I did in a local project I didn’t have the problem