Say you have 10 NEF images, each backed up on card 2 as jpeg large/fine/optimal. What will happen is that after you trash the first set of 10 (I do this individually hitting the "trash" button twice as it requests for each image (slow, but I may change my mind on a delete), you will then see a second set of 10 images listed, but in the lower right-hand corner, instead of it reading "NEF" it will read "Jpeg." Trash these also the same way, and you're clean.
Never criticize a man until you walk a mile in his shoes. Then you'll be a mile away and have his shoes!