Replacing an Open file

We recently were hacked by malware. We repaired our site, but were unable to remove on file en-IS.php. I finally discovered why, the file header.php was edited to include a line that required the presence of the above file in our file structure.

I have the original header.php file without the line added by the hacker. If I try to simple overwrite the file I cannot becuase it is open. What is the best and most graceful way I can get the header.php file closed, so I can replace it.

Do I need to shut down my site temporarily to do this? If som How would I do that?

Thanks

Greg