FileGuard Warnings. . .Critical or False Positive?

I used diffchecker.com to check the files against backups that early morning before, and aren’t seeing anything different between the two files.

If there was something bad in the index.php file, then it would show up on the live side but this is all that I see when opening up the file

<?php
/**
 * Front to the WordPress application. This file doesn't do anything, but loads
 * wp-blog-header.php which does and tells WordPress to load the theme.
 *
 * @package WordPress
 */

/**
 * Tells WordPress to load the WordPress theme and output it.
 *
 * @var bool
 */
define('WP_USE_THEMES', true);

/** Loads the WordPress Environment and Template */
require( dirname( __FILE__ ) . '/wp-blog-header.php' );

You haven’t been hacked.
File Guard detects file change (meta data), as opposed to file modification (content of the file). When migrating the site, the meta data was changed (ctime, inode and maybe onwership too), hence it sent you a few notifications.

You can read more information about it in the doc:

Note that if you updated WordPress, you could receive a few notifications too, for instance, if a visitor accessed a core file that was just updated (e.g., index.php, wp-cron.php, admin-ajax.php etc).

Thanks for the information @nintechnet, I appreciate it!