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Restoring files affected by virus

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Sure hope someone can help. In order to try to keep his computer virus free, my husband doesn't have his main home office computer even hooked up to the internet. SOoooo, we didn't have any ant-virus software running on it - BIG mistake! Recently an office associate recently gave him some files on a USB pen, which apparantly contained a virus. He began constantly getting a DOS window, and the batch file it ran was making a list of all the ".doc" files on his C: drive and all subdirectories, then writing their names to another file. I finally got on AVGs website and figured out how to manually dowload updated virus definitions and install them to his non-internet enabled PC. It found a virus, but only labeled it as "Generic Trojan Horse :NTX". It did get rid of the virus, and we thought the problem was ended. He does keep all his most important files on a different drive, so we didn't notice anything until a few days later when he realized that ALL of his other .doc files on his C: drive were GONE! Poking around the computer, I think I "found" all the files. They are in a strange C:\WINDOWS subdirectory, and all now are .bat files rather than .doc files. I tried to rename some of them, but to no avail. The dates and file sizes are similar to what we would expect if they were the original .doc files.

Can anyone tell me what to do to recover these file?

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