Upgrading CI to last version

No not to just replace the system you also need to replace the index.php file etc;

You can watch the ./application folder for changes, I don't take chances so I
replace the whole framework I have a snippet app that I keep all my framework settings in.

Good grief man, the OP is only going from 3.1.5 to 3.1.7 !

The only reference in the instructions to index.php is the suggestion of temporarily putting a "site closed" static file in place while the upgrade happens. There is no reason to replace the CI index file.

There is no reason for stomp all over the application folder. The two "Upgrading from..." pages have only two steps the first step in each being

Replace all files and directories in your system/ directory.

There is nothing to indicate any files in or subordinate to /application need to be replaced. To my thinking, the chances something will go wrong are greater if you start messing with the /application files & folders. Remember, the OP is not a developer and has no idea what should or should not be in and under /application.