I have an existing ini file that I have created and I would like to know if there was a way to update a section of the file or do I have have to rewrite the entire file each
If you use the PHP INI functions, you must rewrite the file each time.
If you write your own processor, you could (with limitations) update in place. If your insertions are longer or shorter than your deletions, you'll have to rewrite the file anyhow.