Bruth is right. I was just about to post the same thing. We are dealing with a moderate to advanced cracker, with tools he/she probly made. If this person was a hacker, the worst they would do is take the source of the projects or something, and usually only with permission.
I think the first step is to back up, but if you want to find the Cracker, I suggest checking source for the main links and try to chek as many files as we can. If we can find abnormalities, I can help catch this idiot.
I'm sure alot of us could. One thing this person doesn't realize, is that many, many, many of us are programmers. Most of us have basic to great knowledge of how code works and what it should look like. And most of all, alot of us lost important data because of this. Even if it's restored, it's still a waste of time, effort, and energy. So if we find the source of the virus or whatever it is, than we can stop this jerk.
BTW, if it is a virus, there is a chance it will infect your computers. even if not designed to do so, they can come in and ruin text files and such, maybe even system32 files. So scan your PC's for viruses whenever you get the chance.