The position and orientation relative to the layout stays the same, while the position and rotation from the footprint file will update on the layout to reflect footprint changes (if you tell it to.)
In other words, if you edit your footprint to rotate 90 degrees CW and move it 2.54mm to the right in the footprint editor, it will rotate 90 degrees CW and move 2.54mm to the right in the layout (when you update the footprint in the layout).