The most critical time in digital asset management occurs immediately after the photo is taken. The camera transfers it from its internal memory to my compact flash card. If anything interrupts the transfer the image can be corrupted and lost.
I format the card at the time I get my equipment ready. I want the camera I'm using to prepare the card. If the card formats, I have additional assurance that the card is working properly.
I carry my extra cards in container that holds four and has a hard plastic shell. Formatted cards are placed with the Logo on top. As I switch cards, the used cards are placed with the logo down.
Compact flash cards are very sturdy. I've heard of cases where they were laundered and dried and still worked. Their biggest vulnerability is the double row of little holes the bottom edge. These holes need to mate with a matching set of little wires in the camera. If you are careless and get a piece of dirt in one of these holes, you can bend the wire as the card is inserted. None of your cards will work then until the camera is repaired. This is why I'm careful to use a case that provides protection and keeps the cards clean.
Have you noticed that your camera doesn't know precisely how may photos remain. This is because the space a image uses varies. I seldom delete a photo in the camera. When you delete you free up space for another image. When the camera tries to put a new image in the space, it often has to put parts of the picture in more than one place. It handles this task very well but the chances for failure have increased and it takes a little longer to read and write the image.
My Canon cameras can store images in a second directory when certain numbers are reached. If you use a manual download process, it is easy not to notice a few photos in a second directory. You may even reuse the card without realizing images are missing.
I use Downloader Pro for my downloads. It removes human error. It finds all the images. It renames the photos. It builds a folder and places the images into it. If I have a .gpx file, it uses it to add GPS information to each photo. I can even set it up to build a duplicate set of images on a second drive. I have to admit that I thought this program would be a waste of money before I bought it. It wasn't. I'm often pretty tired when I download and Downloader Pro takes human error out of the process.
I realize that Lightroom has similar functionality. The problem with using Lightroom is that my images end up in Lightroom. I want to some sorting and culling before this happens. I'm used to being able to do this rapidly. Lightroom does many things well, but if I put a thousand images in, it takes a long time to remove the 900 that I want taken out.
If you ever have problem downloading images, I've found that the problem is usually in the card reader or the wire that attaches to the PC. If you can see the image in the camera you have some assurance that the image is actually there. Try a different reader and even another PC. If you can't see the image in the camera you have a bigger problem. Verify that you are looking at the correct card. It's possible that the camera malfunctioned and never saved the images. If you, you are out of luck If the images are on the card, you can download some good software that will attempt to recover the images. You can usually verify that it will recover your images before you pay for it. This software also works if you accidently format a card before the images are downloaded.
When my images are downloaded, I leave them on the card until I have two copies of the most important images. The card is my backup until then.