Over time, data stored on writable media subject to virus scans will be deleted or moved regardless of the presence of a virus. This is due to the ever-expanding definition of what is a virus and through heuristic analysis. In other words, what was not considered a virus in the past may be considered one in the future despite its legitimacy.
So what can we do about it?
One way is to routinely back-up to an optical disk or some other write-once media. However, CDFS, the file system used on CDs and DVDs allows files up to 2GB. Large files have to be kept another way. There may be hope though. As file permissions and firewalls get safer in Vista it may be possible to set aside areas on your PC that do not get virus checked.