I asked the question, and I can now answer it for everyone's benefit: the pictures are not lost!
Even though the photos did not show up in iphoto, they were all in the library. I looked under Finder / Today and found the files there. By clicking one of the pictures I could see where they were stored, and it was inside the iphoto library. However, I had to copy all the pictures to a folder in my desktop and re-import them into iphoto in order to see them in the software. I'm not sure why that is, but I don't really care as long as I haven't lost the pictures!