Is there a way to prevent this?
Did you try turning off snap by clicking on View > Snap?
Turned off all Snaps but when I move the duplicated group from file A to an artboard in file B, everything still gets centered.
Fwiw, when the layers are duplicated into file B and before it's in a specific artboard, the duplicated objects are all in the right place. But it's when dragging the duplicated objects into an artboard in File B, when all the individual layers in the group gets centered and not in its original positions.