I'm pretty new to Git (and version control in general) and am ashamed to say that this problem has been going on for a while now. Occasionally, after adding changes, git will delete everything from my repository upon the following commit.
Afterward I add and commit again, and it creates everything it just deleted.
It hasn't caused any issues, but I can't imagine this is a good thing, and I'm beginning to get more and more freaked out by it.
Oops. I'm just using the commands:
git add .
git commit -m "blah blah"