"codeigniter/application/" is for your application.
It is copied from "vendor/codeigniter/application/" at your first installation.
Files in it is not changed if you run "composer update".
"vendor/codeigniter/" is the official CodeIgniter source code.
All files in "vendor/codeigniter/" are updated when you "composer update" if CodeIgniter new version is available.
In short, you don't worry about "vendor/codeigniter/application/". You are not using it.
And "vendor/" is Composer vendor folder. You should not edit any files in it.