Not an answer, but a suggestion in change of workflow. There are many different cards, and many different cameras, and not all of them work exactly the same. For this reason, the generally prefered practice is to simply eject the card from within Aperture, and then (when needed) reformat the card in the camera that you will be using it in.
As a bonus, this gives you additional copies of your digital camera files until you reformat the card. I suggest that you have at least two copies of your file, on separate drives (or other storage media) at all times.
I don't know why your files are not being deleted.