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im not quite sure yet why this happens, but here is what you need to do.
first select your target mesh and using alt+A align the target mesh to the original mesh in the x,y, and z positions and orientation. then select the target mesh, turn off the skin modifier (as well as any other modifiers that you have in the stack), go to the hierarchy panel and select "affect object only", then "center to pivot". that should do it.
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