Reading a CF directly into Aperture or any other images management app is poor workflow. Try this:
• Copy from CF card to a folder on a hard drive. Best is using a card reader but camera to hard drive works.
• EJECT the CF card and put it safely aside after copying. Very important step to avoid potential errors.
• Back up the folder of images to a separate drive.
• After that last step it is safe to reformat the CF card in-camera.
• Now import into Aperture from the folder of images on the hard drive.
Note that any workflow that imports directly into Aperture or any other images management app puts original image files at risk and is just WRONG, even though even the Aperture manual suggests such workflows. We have had scores (if not hundreds) of posts here that have been variants on "Aperture ate my originals," all of which could have been avoided by the proper workflow above.
Good luck! Let us know if the above workflow does not work. It has worked for years with my D2x.
Of course those with two-card cameras have the luxury of creating all kinds of safe workflows different than the above.