Well, I backed everything up and did a clean install of my OS to clear up clutter. I started loading my games from Steam and when I copied my saves for Dark Souls, they aren't recognized. At this point, I'm redownloading BL2 and I'm nervous about it not accepting my profile.bin file so the golden keys I've been hoarding will be lost.
I guess this is a good time to start a fresh character on Dark Souls, but it hurts to have lost some of the items that I had gotten. From here on out, I'm going to backup my saves on multiple devices to prevent this from happening again. Before anyone asks, I copied the whole NBGI folder so I should be able to have been able to overlay it.