I have my two memory cards set to backup. When I delete a few photos, I don't see them in the camera. When I download from the camera, I see my deleted photos. Guess when you delete, it's for only one slot?
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!
Or - if you format the card in the camera, which I do after importing the images to my computer AND backing them up to an external drive, you format each card separately. On my D7000, after you press the two red buttons on the camera, the top LCD gives you a choice of which card to format via an indicator on the right edge of the screen. Use the control wheel to select one, then press the two red buttons again to complete the format. Repeat and select the other card.