You could try:
Check for multiple photo folders. My camera re-sets its folder in use every so often. It can also be done on purpose (and on accident).
View the photos from in the camera (on the camera).
If they are there: attach your camera to your PC instead of using the card reader. Not as fast a transfer, but it works
If they are not there when viewed from the camera and there is no other folder, you could try data recovery such as PhotoRec.
data recover