For a system of particles/bodies, the centre of mass depends on how mass is distributed. When mass leaves a system asymmetrically (e.g. draining from the bottom), the COM shifts toward the remaining mass. As the shape of the remaining water column changes over time, the COM's position traces a path that depends on the geometry of drainage, not just the total mass remaining.
Initially the sphere is full of water and both the shell and the water are symmetric about the centre, so the COM of the whole...
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