This article is from the Computer Viruses FAQ, by Nick FitzGerald n.fitzgerald@csc.canterbury.ac.nz with numerous contributions by others.
Many things apart from viruses cause corruption of file systems.
With DOS machines possibly the most common is Microsoft's SmartDrive
disk cache program that came with Microsoft Windows 3.1 and subsequent
versions of MS-DOS. Most versions of this software not only cache disk-
reads but, by default, also cache disk-writes. This means that recently
"written" files (say from saving a document in your word processor) may
not have all the information about the associated file system updates
written to disk by the time you exit the application, close Windows and
turn off your PC. Users who simply save work then turn their PC off are
even more likely to suffer from disk caching induced problems like this.
Regardless of what caused your file-system corruption, you should
probably seek expert help *before* trying to fix anything yourself.
While there are many powerful and interesting-sounding utilities of the
"disk fix" kind available, *all* of these have the stunning ability to
render your file system all but unfixable (or at least, fixable to a
much lesser degree) when presented with unusual situations their authors
hadn't considered when designing the programs. Unfortunately, as these
programs (by definition) do not recognize these situations, they
confidently pronounce that you have such-and-such a problem then ask
your permission to fix it. Even when these utilities have "undo"
options, they often cannot restore your file system to its originally
"broken" state to give human experts their best shot at fixing it.
Thus, detecting whether it is safe to let one of these programs loose on
your disks is something you should normally seek expert help in
deciding.
 
Continue to: