I've never worked with charcater encoding so I can't help you with that part but automating the editing of multiple files, can I suggest writing a PHP script that opens every file, reads the contents, converts the contents to UTF-8 (I don't know how to do that part), and re-writing the file?
You could manually list all the file names and build an array at the beginning of your script with all the file names or you could use the exec command to do an "ls" to list all the filenames an obtain a list of files automatically.
I understand that there is a PHP module called mbstring that allows the PHP script to work in different character encodings so you might need to have that installed to accomplish the character conversion... but now I'm talking about stuff that I don't know anything about. Sorry, I can't help more than that.