In reply to Ben Watts:
You might find that you have two sets of files (CR2 & JPEG) with an equal number in each. If so, the camera has captured two file formats for each photo that has been taken. If that is the case, then you haven't actually 'lost' any photo's.
Ultimately, you would be better off editing the CR2 file and getting a program for doing that, but in the meantime, just open the JPEG's as you normally would.