This issue has been frustrating me for the past hour until I realized the only thing left different between my last good copy and my debug ‘in and out’ copy that was still offset by a good meter or so was the Outside Behavior setting.
Easy reproduction steps: Generate a heightmap, bring it into UE4 and set a static marker where you can easily notice a shift in the terrain, import that heightmap back into WM using Mirror outside behavior, output it with no other processing, import the new ‘unchanged’ heightmap into UE4 and notice that the heightmap has shifted past your static marker.