If these were originals, then the idiosyncrasies of journaling file systems (such as NTFS) should provide for a relatively easy method of recovering data for someone familiar with either the software called "System Mechanics Search and Recovery" or a Unix based operating system such as Linux. The first option is simpler but not free, and can be somewhat counter productive without a second Windows installation as the latter of the two can be done using a live disc instead, but I wouldn't be surprised if you already knew this. As you stated prior, you already know how to travel back in time via Gallifreyan technology, so learning how to operate a flux capacitor would be a waste of your time like reading this paragraph probably was. Just avoid using that vortex manipulator (Windows system restore) as it has nasty side effects and is bad for the heath of Windows.
As for identifying the potential causes of your mishap, this would be nearly impossible without more information as it could be almost anything. Other than reviewing system logs and checking the Virus Vault, there isn't much else that I can suggest. If this was SRB2 related, the error would have likely appeared in the log file. Assuming you have a firewall and the files weren't falsely determined by AVG to be infectious (due to uncommon compression and/or encryption), I guess the only other software related possibility I can thing of is that somehow the attributes of the files were changed to make them hidden. If the issue persist with other files seemly at random, it could be a sign of hard drive failure, though I doubt it would be this. When you have eliminated the impossible, whatever remains, however improbable, must be the truth. -Sherlock Holmes (Chap. 6, p. 111)