You know, I've tried many different shoes in many different sizes, but no matter what I do I seem to lose nails. It doesn't happen right away. I'll run a race and a few weeks later a nail pops off. Now, I say pops off, but what I really mean is that the nail starts to come loose at the top and I help it off by pulling, prying and clipping until it's gone. It doesn't hurt. My toes don't hurt when I run long, and the nail coming off doesn't hurt, so mostly I don't even worry about it. I have recently purchased some new trail runners with a bit of a wider toe box, so maybe that will help. Who knows? For now, me and my toenail will just enjoy this closed toe shoe weather.
For the record, I actually have four whole toenails at the moment. One on my left foot, and three on my right.