This may not solve your problem, but you should feed the video files into a diagnostic utility like the ones listed here http://www.moviecodec.com/topics/61931p1.html to check their integrity. Some viruses will deliberately destroy certain file types (I think one of the early worms used to destroy mp3 files).
If it recognizes the files as AVI with the xvid codec, then I’m not sure what to suggest.
BTW what error message(s) are you getting? If it’s an access denied, it may simply be because of the reformat. You would need to take ownership of the files again to be able to access them. http://support.microsoft.com/kb/308421
So i use the video editing software vegas 5.0 alot, ive used it before and not had this problem. i used avi splitter to cut big movies into small portions and it used to work fine, but my main drive got a bunch of malware on it and i had to wipe my c drive (my video files were on a different drive) i reinstalled vegas and now none of my splits work (they are all in xvid) ive tried every converter and downloaded every xvid and divx codec but still no video in vegas. Does anyone know one that actually works?