As far as I know there isn't a tool specifically designed to do this, however, if you want to delve into Linux a little bit, I would suggest creating a script using
sed and possibly
grep to search for and replace all of the incorrect entries. However, this method might still take a while especially if you don't have much experience with the command line or shell scripting.
Alternatively, I believe IDEs such as Dreamweaver and whatnot have the ability to rename a file and update all of the references, so you may look into that. It means that you would have to do it for every file, but it might still be faster than trying to write a script that would catch all possible cases. Aptana is another IDE that might do this, although I have not used it for said purpose.