Just to make sure I was clear...
Even if you don't care about the photos you don't see anymore, you'll still want to reformat that card using the camera's menu choice for format before using it again.
Otherwise, you're probably going to have corrupted and/or missing images for the new ones you're taking, too (where you'll end up with images that look like part of them are missing, etc.). It's obvious from your description that your file system is corrupted. Formatting the card using the camera's menu choice for format (and use the camera's menu choice for format, not a PC) will create a new File Allocation Table. But, recover any images you want from it first using the photorec tool mentioned in this link:
Recovering Images or Video from Memory Cards
Then, *after* you recover all of the images from it (and you'll probably see a lot of them if you've used it a lot, since it will recover deleted images from it, too) use your camera's menu choice for Format before you use it again. But, again, even if you don't care about the images you lost and don't want to bother recovering them, reformat it using the camera's menu choice for Format before using it again anyway (and I do that *every* time I reuse a memory card, no exceptions). Otherwise, you'll continue to have problems with it.