It is best to make any changes to the contents of the card in the camera, not in the computer. Deleting and reformatting modify the directory on the card which is its index or table of contents. If there is any software incompatibility between the computer and the camera, things can get quite mixed up.
I have had 100% success using a CF reader to transfer all images to the computer, then returning the card with its contents unchanged to the camera. After I check the images on the computer (and make a backup if I'm not doing this in the field) I reformat the card in the camera. Reformatting (rather than deleting images) creates a new directory which is a clean way to start the next batch of images. I have never had any reason to keep images on a card once they have been moved to the computer.
Regards,
Roy