Earlier quoted context omitted.
Did you file a support ticket for this? It sounds like an unrelated problem. We can investigate if you let us know what repo is causing the problem. Visit http://support.github.com or email support@github.com.
I posted the name of the repo to the thread, and someone else on the thread is confirming the same problem.
It turns out that GitHub didn't lose any of my commits. All future readers should ignore my comments on this.