Will mass deleting WP Users then reimporting CSV with the same userid break WP?

You don’t need to re-import the CSV to add metas. Assuming you want to do this for every user on the site here is what you do.

$users = get_users(); // this will get all users on your site.

// loop through each user updating their meta
foreach( $users as $user ) {
     // whatever key/value pair you want to add to each user
     // you can have as many as you want
     update_user_meta( $user->ID, $meta_key, $meta_value );
}

Put this in your theme’s functions.php file and load your site ONCE. Because this temporary code will execute on each page load so just load it once and remove this code. This will successfully add the meta you want to each user.