Again, the penalty is NOT for leaving empties in the discarded gun, it's for NOT CYCLING THE ACTION.
SHB Pg, 28
You need to get your head away from what's in the discarded gun, and look to, has the action been cycled. As there is no action to cycle in a SxS, it must be emptied.
All long guns, lever, pump or sxs, with a live round in the chamber is a SDQ penalty.