"I" didn't delete it, it was either another user (though I doubt it), the trojan itself, or the process of removing the trojan; I don't think these last two are very likely either, but something/someone did in fact delete it.

Like I mentioned before, this is my backup drive. I had most of the things I wanted to keep in this folder: pictures, emails, documents, presentations, etc.

The good news is, I can get the majority of it back; it will just take some time restoring them one-by-one.